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8
.dockerignore
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.direnv
.github
.pytest_cache
.vscode
docs
hardware
nix
software

13
.editorconfig
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# SPDX-License-Identifier: CC-BY-SA-4.0
root = true
[*]
end_of_line = lf
insert_final_newline = true
trim_trailing_whitespace = true
charset = utf-8
[*.nix]
indent_style = tab
indent_size = 2

11
.envrc
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# SPDX-License-Identifier: GPL-3.0-or-later
# https://github.com/direnv/direnv/wiki
use flake
layout python3
watch_file ./nix/shell.nix
eval "$shellHook"

24
.github/ISSUE_TEMPLATE/feature_request.md vendored
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<!--
SPDX-License-Identifier: CC-BY-SA-4.0
-->
---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: enhancement
assignees: ''
---
**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**
A clear and concise description of what you want to happen.
**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.
**Additional context**
Add any other context or screenshots about the feature request here.

37
.github/ISSUE_TEMPLATE/hardware-bug-report.md vendored
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<!--
SPDX-License-Identifier: CC-BY-SA-4.0
-->
---
name: Hardware bug report
about: Create a hardware bug report to help us
title: ''
labels: bug, hardware
assignees: ''
---
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1.
2.
3.
**Expected behavior**
A clear and concise description of what you expected to happen.
**Pictures**
If applicable, add pictures to help explain your problem.
**Additional context**
Add any other context about the problem here.
**Planktoscope version (please complete the following information):**
- Raspberry version: [e.g. Pi4]
- OS: [Custom or standard image]
- Stepper motor hat [e.g. Adafruit or other]
- Version [e.g. 2.0]

31
.github/ISSUE_TEMPLATE/software-bug-report.md vendored
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<!--
SPDX-License-Identifier: CC-BY-SA-4.0
-->
---
name: Software bug report
about: Create a report to help us
title: ''
labels: bug, software
assignees: ''
---
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error
**Expected behavior**
A clear and concise description of what you expected to happen.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Additional context**
Add any other context about the problem here.

32
.github/workflows/auto-label.yml vendored
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name: Auto Assign to Projects based on software/hardware label
on:
issues:
types: [labeled]
pull_request:
types: [labeled]
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
jobs:
assign_one_project:
runs-on: ubuntu-latest
name: Assign to projects based on label
steps:
- name: Assign issues and pull requests with `hardware` label to project `Hardware`
uses: srggrs/assign-one-project-github-action@1.2.0
if: |
contains(github.event.issue.labels.*.name, 'hardware') ||
contains(github.event.pull_request.labels.*.name, 'hardware')
with:
project: 'https://github.com/PlanktonPlanet/PlanktoScope/projects/2'
column_name: 'Bugs'
- name: Assign issues and pull requests with `software` label to project `Sofware`
uses: srggrs/assign-one-project-github-action@1.2.0
if: |
contains(github.event.issue.labels.*.name, 'software') ||
contains(github.event.pull_request.labels.*.name, 'software')
with:
project: 'https://github.com/PlanktonPlanet/PlanktoScope/projects/1'
column_name: 'To Do'

61
.github/workflows/docs.yml vendored
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name: release docs
on:
push:
tags:
- hatch-v*
- hatchling-v*
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
- name: Ensure latest pip
run: python -m pip install --upgrade pip
- name: Install env
run: pip install -e .
- name: Configure Git for GitHub Actions bot
run: |
git config --local user.name 'github-actions[bot]'
git config --local user.email 'github-actions[bot]@users.noreply.github.com'
- name: Build documentation
run: hatch run docs:build
env:
GH_TOKEN_MKDOCS_MATERIAL_INSIDERS: ${{ secrets.GH_TOKEN_MKDOCS_MATERIAL_INSIDERS }}
- name: Create archive
run: git archive -o site.zip gh-pages
- uses: actions/upload-artifact@v3
with:
name: documentation
path: site.zip
publish:
runs-on: ubuntu-latest
needs:
- build
steps:
- uses: actions/download-artifact@v3
with:
name: documentation
- name: Unpack archive
run: python -m zipfile -e site.zip site
- uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: site
commit_message: ${{ github.event.head_commit.message }}
enable_jekyll: false
allow_empty_commit: false

16
.github/workflows/reuse.yml vendored
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@ -1,16 +0,0 @@
---
# SPDX-FileCopyrightText: 2022 Free Software Foundation Europe e.V. <https://fsfe.org>
#
# SPDX-License-Identifier: CC0-1.0
name: REUSE Compliance Check
on: [push, pull_request]
jobs:
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: REUSE Compliance Check
uses: fsfe/reuse-action@v1

43
.github/workflows/test.yml vendored
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@ -1,43 +0,0 @@
---
name: test
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]
concurrency:
group: test-${{ github.head_ref }}
cancel-in-progress: true
env:
PYTHONUNBUFFERED: "1"
FORCE_COLOR: "1"
jobs:
run:
name: |
Python ${{ matrix.python-version }} on
${{ startsWith(matrix.os, 'macos-') &&
'macOS' || startsWith(matrix.os, 'windows-') && 'Windows' || 'Linux' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install Hatch
run: pip install --upgrade hatch
- name: Run tests
run: hatch run cov

31
.gitignore vendored
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# General
*.dll
*.log
*.so
*.swp
export
img
tmp
# Nix
.direnv
.pre-commit-config.yaml
result
# Python
/*.py[cod]
/__pycache__
/.benchmark
/.coverage*
/.pytest_cache
# Node-Red
/.main.json.backup
/flow_backup.json
# Mkdocs
dist
docs/_*
site
TODOS.md

31
.reuse/dep5
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Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: PlanktoScope
Upstream-Contact: Thibaut Pollina <planktoscope@gmail.com>
Source: https://github.com/PlanktoScope/PlanktoScope
Files: hardware/*
Copyright: (C) 2020-2023 Romain Bazile
License: CERN-OHL-S-2.0
Files:
.github
.vscode
.dockerignore
.editorconfig
.envrc
.gitignore
flake.*
nix/*
Dockerfile
pyproject.toml
okh.toml
mkdocs.yml
software/*
Copyright: (C) 2020-2023 Romain Bazile, Sebastian Wendel
License: GPL-3.0-or-later
Files:
docs/*
README.md
Copyright: (C) 2020-2023 Romain Bazile, Thibaut Pollina, Adam Larson, Will Major, Sebastian Wendel
License: CC-BY-SA-4.0

20
.vscode/extensions.json vendored
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{
"recommendations": [
"bungcip.better-toml",
"cab404.vscode-direnv",
"davidanson.vscode-markdownlint",
"editorconfig.editorconfig",
"esbenp.prettier-vscode",
"exiasr.hadolint",
"kamadorueda.alejandra",
"kamikillerto.vscode-colorize",
"mechatroner.rainbow-csv",
"ms-python.black-formatter",
"ms-python.python",
"oderwat.indent-rainbow",
"pinage404.nix-extension-pack",
"redhat.vscode-yaml",
"yatki.vscode-surround",
"yzhang.markdown-all-in-one",
],
}

21
.vscode/settings.json vendored
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@ -1,21 +0,0 @@
{
"[nix]": {
"editor.defaultFormatter": "kamadorueda.alejandra",
"editor.formatOnSave": true,
},
"[toml]": {
"editor.formatOnSave": true,
"editor.insertSpaces": true,
"editor.codeLens": true
},
"yaml.schemas": {
"https://squidfunk.github.io/mkdocs-material/schema.json": "mkdocs.yml",
},
"yaml.customTags": [
"!ENV scalar",
"!ENV sequence",
"tag:yaml.org,2002:python/name:materialx.emoji.to_svg",
"tag:yaml.org,2002:python/name:materialx.emoji.twemoji",
"tag:yaml.org,2002:python/name:pymdownx.superfences.fence_code_format"
]
}

5
Dockerfile
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FROM nginx:alpine
WORKDIR /usr/share/nginx/html
COPY ./site /usr/share/nginx/html

0
LICENSES/CC-BY-SA-4.0.txt → LICENSE
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121
LICENSES/CC0-1.0.txt
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@ -1,121 +0,0 @@
Creative Commons Legal Code
CC0 1.0 Universal
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REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
HEREUNDER.
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These owners may contribute to the Commons to promote the ideal of a free
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For these and/or other purposes and motivations, and without any
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vii. other similar, equivalent or corresponding rights throughout the
world based on applicable law or treaty, and any national
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2. Waiver. To the greatest extent permitted by, but not in contravention
of, applicable law, Affirmer hereby overtly, fully, permanently,
irrevocably and unconditionally waives, abandons, and surrenders all of
Affirmer's Copyright and Related Rights and associated claims and causes
of action, whether now known or unknown (including existing as well as
future claims and causes of action), in the Work (i) in all territories
worldwide, (ii) for the maximum duration provided by applicable law or
treaty (including future time extensions), (iii) in any current or future
medium and for any number of copies, and (iv) for any purpose whatsoever,
including without limitation commercial, advertising or promotional
purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each
member of the public at large and to the detriment of Affirmer's heirs and
successors, fully intending that such Waiver shall not be subject to
revocation, rescission, cancellation, termination, or any other legal or
equitable action to disrupt the quiet enjoyment of the Work by the public
as contemplated by Affirmer's express Statement of Purpose.
3. Public License Fallback. Should any part of the Waiver for any reason
be judged legally invalid or ineffective under applicable law, then the
Waiver shall be preserved to the maximum extent permitted taking into
account Affirmer's express Statement of Purpose. In addition, to the
extent the Waiver is so judged Affirmer hereby grants to each affected
person a royalty-free, non transferable, non sublicensable, non exclusive,
irrevocable and unconditional license to exercise Affirmer's Copyright and
Related Rights in the Work (i) in all territories worldwide, (ii) for the
maximum duration provided by applicable law or treaty (including future
time extensions), (iii) in any current or future medium and for any number
of copies, and (iv) for any purpose whatsoever, including without
limitation commercial, advertising or promotional purposes (the
"License"). The License shall be deemed effective as of the date CC0 was
applied by Affirmer to the Work. Should any part of the License for any
reason be judged legally invalid or ineffective under applicable law, such
partial invalidity or ineffectiveness shall not invalidate the remainder
of the License, and in such case Affirmer hereby affirms that he or she
will not (i) exercise any of his or her remaining Copyright and Related
Rights in the Work or (ii) assert any associated claims and causes of
action with respect to the Work, in either case contrary to Affirmer's
express Statement of Purpose.
4. Limitations and Disclaimers.
a. No trademark or patent rights held by Affirmer are waived, abandoned,
surrendered, licensed or otherwise affected by this document.
b. Affirmer offers the Work as-is and makes no representations or
warranties of any kind concerning the Work, express, implied,
statutory or otherwise, including without limitation warranties of
title, merchantability, fitness for a particular purpose, non
infringement, or the absence of latent or other defects, accuracy, or
the present or absence of errors, whether or not discoverable, all to
the greatest extent permissible under applicable law.
c. Affirmer disclaims responsibility for clearing rights of other persons
that may apply to the Work or any use thereof, including without
limitation any person's Copyright and Related Rights in the Work.
Further, Affirmer disclaims responsibility for obtaining any necessary
consents, permissions or other rights required for any use of the
Work.
d. Affirmer understands and acknowledges that Creative Commons is not a
party to this document and has no duty or obligation with respect to
this CC0 or use of the Work.

289
LICENSES/CERN-OHL-S-2.0.txt
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@ -1,289 +0,0 @@
CERN Open Hardware Licence Version 2 - Strongly Reciprocal
Preamble
CERN has developed this licence to promote collaboration among
hardware designers and to provide a legal tool which supports the
freedom to use, study, modify, share and distribute hardware designs
and products based on those designs. Version 2 of the CERN Open
Hardware Licence comes in three variants: CERN-OHL-P (permissive); and
two reciprocal licences: CERN-OHL-W (weakly reciprocal) and this
licence, CERN-OHL-S (strongly reciprocal).
The CERN-OHL-S is copyright CERN 2020. Anyone is welcome to use it, in
unmodified form only.
Use of this Licence does not imply any endorsement by CERN of any
Licensor or their designs nor does it imply any involvement by CERN in
their development.
1 Definitions
1.1 'Licence' means this CERN-OHL-S.
1.2 'Compatible Licence' means
a) any earlier version of the CERN Open Hardware licence, or
b) any version of the CERN-OHL-S, or
c) any licence which permits You to treat the Source to which
it applies as licensed under CERN-OHL-S provided that on
Conveyance of any such Source, or any associated Product You
treat the Source in question as being licensed under
CERN-OHL-S.
1.3 'Source' means information such as design materials or digital
code which can be applied to Make or test a Product or to
prepare a Product for use, Conveyance or sale, regardless of its
medium or how it is expressed. It may include Notices.
1.4 'Covered Source' means Source that is explicitly made available
under this Licence.
1.5 'Product' means any device, component, work or physical object,
whether in finished or intermediate form, arising from the use,
application or processing of Covered Source.
1.6 'Make' means to create or configure something, whether by
manufacture, assembly, compiling, loading or applying Covered
Source or another Product or otherwise.
1.7 'Available Component' means any part, sub-assembly, library or
code which:
a) is licensed to You as Complete Source under a Compatible
Licence; or
b) is available, at the time a Product or the Source containing
it is first Conveyed, to You and any other prospective
licensees
i) as a physical part with sufficient rights and
information (including any configuration and
programming files and information about its
characteristics and interfaces) to enable it either to
be Made itself, or to be sourced and used to Make the
Product; or
ii) as part of the normal distribution of a tool used to
design or Make the Product.
1.8 'Complete Source' means the set of all Source necessary to Make
a Product, in the preferred form for making modifications,
including necessary installation and interfacing information
both for the Product, and for any included Available Components.
If the format is proprietary, it must also be made available in
a format (if the proprietary tool can create it) which is
viewable with a tool available to potential licensees and
licensed under a licence approved by the Free Software
Foundation or the Open Source Initiative. Complete Source need
not include the Source of any Available Component, provided that
You include in the Complete Source sufficient information to
enable a recipient to Make or source and use the Available
Component to Make the Product.
1.9 'Source Location' means a location where a Licensor has placed
Covered Source, and which that Licensor reasonably believes will
remain easily accessible for at least three years for anyone to
obtain a digital copy.
1.10 'Notice' means copyright, acknowledgement and trademark notices,
Source Location references, modification notices (subsection
3.3(b)) and all notices that refer to this Licence and to the
disclaimer of warranties that are included in the Covered
Source.
1.11 'Licensee' or 'You' means any person exercising rights under
this Licence.
1.12 'Licensor' means a natural or legal person who creates or
modifies Covered Source. A person may be a Licensee and a
Licensor at the same time.
1.13 'Convey' means to communicate to the public or distribute.
2 Applicability
2.1 This Licence governs the use, copying, modification, Conveying
of Covered Source and Products, and the Making of Products. By
exercising any right granted under this Licence, You irrevocably
accept these terms and conditions.
2.2 This Licence is granted by the Licensor directly to You, and
shall apply worldwide and without limitation in time.
2.3 You shall not attempt to restrict by contract or otherwise the
rights granted under this Licence to other Licensees.
2.4 This Licence is not intended to restrict fair use, fair dealing,
or any other similar right.
3 Copying, modifying and Conveying Covered Source
3.1 You may copy and Convey verbatim copies of Covered Source, in
any medium, provided You retain all Notices.
3.2 You may modify Covered Source, other than Notices, provided that
You irrevocably undertake to make that modified Covered Source
available from a Source Location should You Convey a Product in
circumstances where the recipient does not otherwise receive a
copy of the modified Covered Source. In each case subsection 3.3
shall apply.
You may only delete Notices if they are no longer applicable to
the corresponding Covered Source as modified by You and You may
add additional Notices applicable to Your modifications.
Including Covered Source in a larger work is modifying the
Covered Source, and the larger work becomes modified Covered
Source.
3.3 You may Convey modified Covered Source (with the effect that You
shall also become a Licensor) provided that You:
a) retain Notices as required in subsection 3.2;
b) add a Notice to the modified Covered Source stating that You
have modified it, with the date and brief description of how
You have modified it;
c) add a Source Location Notice for the modified Covered Source
if You Convey in circumstances where the recipient does not
otherwise receive a copy of the modified Covered Source; and
d) license the modified Covered Source under the terms and
conditions of this Licence (or, as set out in subsection
8.3, a later version, if permitted by the licence of the
original Covered Source). Such modified Covered Source must
be licensed as a whole, but excluding Available Components
contained in it, which remain licensed under their own
applicable licences.
4 Making and Conveying Products
You may Make Products, and/or Convey them, provided that You either
provide each recipient with a copy of the Complete Source or ensure
that each recipient is notified of the Source Location of the Complete
Source. That Complete Source is Covered Source, and You must
accordingly satisfy Your obligations set out in subsection 3.3. If
specified in a Notice, the Product must visibly and securely display
the Source Location on it or its packaging or documentation in the
manner specified in that Notice.
5 Research and Development
You may Convey Covered Source, modified Covered Source or Products to
a legal entity carrying out development, testing or quality assurance
work on Your behalf provided that the work is performed on terms which
prevent the entity from both using the Source or Products for its own
internal purposes and Conveying the Source or Products or any
modifications to them to any person other than You. Any modifications
made by the entity shall be deemed to be made by You pursuant to
subsection 3.2.
6 DISCLAIMER AND LIABILITY
6.1 DISCLAIMER OF WARRANTY -- The Covered Source and any Products
are provided 'as is' and any express or implied warranties,
including, but not limited to, implied warranties of
merchantability, of satisfactory quality, non-infringement of
third party rights, and fitness for a particular purpose or use
are disclaimed in respect of any Source or Product to the
maximum extent permitted by law. The Licensor makes no
representation that any Source or Product does not or will not
infringe any patent, copyright, trade secret or other
proprietary right. The entire risk as to the use, quality, and
performance of any Source or Product shall be with You and not
the Licensor. This disclaimer of warranty is an essential part
of this Licence and a condition for the grant of any rights
granted under this Licence.
6.2 EXCLUSION AND LIMITATION OF LIABILITY -- The Licensor shall, to
the maximum extent permitted by law, have no liability for
direct, indirect, special, incidental, consequential, exemplary,
punitive or other damages of any character including, without
limitation, procurement of substitute goods or services, loss of
use, data or profits, or business interruption, however caused
and on any theory of contract, warranty, tort (including
negligence), product liability or otherwise, arising in any way
in relation to the Covered Source, modified Covered Source
and/or the Making or Conveyance of a Product, even if advised of
the possibility of such damages, and You shall hold the
Licensor(s) free and harmless from any liability, costs,
damages, fees and expenses, including claims by third parties,
in relation to such use.
7 Patents
7.1 Subject to the terms and conditions of this Licence, each
Licensor hereby grants to You a perpetual, worldwide,
non-exclusive, no-charge, royalty-free, irrevocable (except as
stated in subsections 7.2 and 8.4) patent license to Make, have
Made, use, offer to sell, sell, import, and otherwise transfer
the Covered Source and Products, where such licence applies only
to those patent claims licensable by such Licensor that are
necessarily infringed by exercising rights under the Covered
Source as Conveyed by that Licensor.
7.2 If You institute patent litigation against any entity (including
a cross-claim or counterclaim in a lawsuit) alleging that the
Covered Source or a Product constitutes direct or contributory
patent infringement, or You seek any declaration that a patent
licensed to You under this Licence is invalid or unenforceable
then any rights granted to You under this Licence shall
terminate as of the date such process is initiated.
8 General
8.1 If any provisions of this Licence are or subsequently become
invalid or unenforceable for any reason, the remaining
provisions shall remain effective.
8.2 You shall not use any of the name (including acronyms and
abbreviations), image, or logo by which the Licensor or CERN is
known, except where needed to comply with section 3, or where
the use is otherwise allowed by law. Any such permitted use
shall be factual and shall not be made so as to suggest any kind
of endorsement or implication of involvement by the Licensor or
its personnel.
8.3 CERN may publish updated versions and variants of this Licence
which it considers to be in the spirit of this version, but may
differ in detail to address new problems or concerns. New
versions will be published with a unique version number and a
variant identifier specifying the variant. If the Licensor has
specified that a given variant applies to the Covered Source
without specifying a version, You may treat that Covered Source
as being released under any version of the CERN-OHL with that
variant. If no variant is specified, the Covered Source shall be
treated as being released under CERN-OHL-S. The Licensor may
also specify that the Covered Source is subject to a specific
version of the CERN-OHL or any later version in which case You
may apply this or any later version of CERN-OHL with the same
variant identifier published by CERN.
8.4 This Licence shall terminate with immediate effect if You fail
to comply with any of its terms and conditions.
8.5 However, if You cease all breaches of this Licence, then Your
Licence from any Licensor is reinstated unless such Licensor has
terminated this Licence by giving You, while You remain in
breach, a notice specifying the breach and requiring You to cure
it within 30 days, and You have failed to come into compliance
in all material respects by the end of the 30 day period. Should
You repeat the breach after receipt of a cure notice and
subsequent reinstatement, this Licence will terminate
immediately and permanently. Section 6 shall continue to apply
after any termination.
8.6 This Licence shall not be enforceable except by a Licensor
acting as such, and third party beneficiary rights are
specifically excluded.

232
LICENSES/GPL-3.0-or-later.txt
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@ -1,232 +0,0 @@
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for software and other kinds of works.
The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.
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Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS
0. Definitions.
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You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.
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When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.
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You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
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b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
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7. Additional Terms.
“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
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All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
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Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
11. Patents.
A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”.
A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.

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# PlanktoScope: Open and Affordable Quantitative Imaging Platform
# planktoscope-build-workshop
![planktoscope_hero](docs/images/project_description/planktoscope_hero.png)
## What are Plankton?
_"Drifting endlessly, midway between the sea of air above and the depths of the abyss below, these strange creatures and the marine inflorescence that sustains them are called 'plankton' — the wanderers"_ - **[Rachel Carson](https://de.wikipedia.org/wiki/Rachel_Carson)**
Plankton are tiny organisms that drift in the oceans and play a crucial role in the global ecosystem. They are responsible for fixing 30-50% of the world's carbon dioxide and form the foundation of the global food chain. Despite their importance, studying plankton can be challenging due to the vast area of the oceans and the limited resources of research fleets and specialized equipment. The PlanktoScope is an open-source hardware and software platform that aims to make it easier to study plankton by providing high-throughput quantitative imaging capabilities at a low cost.
![planktoscope_hero](docs/images/project_description/planktoscope_architecture.png)
## What is a PlanktoScope?
The PlanktoScope is a modular, open-source platform for high-throughput quantitative imaging of plankton samples. Its small size, ease of use, and low cost make it suitable for a variety of applications, including the monitoring of laboratory cultures or natural micro-plankton communities. It can be controlled from any WiFi-enabled device and can be easily reconfigured to meet the changing needs of the user.
[Learn more about how it works](https://www.planktoscope.org/how-it-works)
## Read the Paper
The PlanktoScope has been described in the article ["PlanktoScope: Affordable Modular Quantitative Imaging Platform for Citizen Oceanography"](https://www.frontiersin.org/articles/10.3389/fmars.2022.949428/full), published in Frontiers in Marine Science in July 2022.
DOI: [https://doi.org/10.3389/fmars.2022.949428](https://doi.org/10.3389/fmars.2022.949428)
## Key Features
Here are some key features of the PlanktoScope:
1. **Low cost**: The PlanktoScope is designed to be affordable, with parts costing under $1000.
2. **Modular**: The PlanktoScope is modular, meaning it can be easily reconfigured to meet the changing needs of users.
3. **Open-source**: The PlanktoScope is based on open-source hardware and software, making it accessible to a wide community of engineers, researchers, and citizens.
4. **Versatility**: The PlanktoScope is versatile, and can be used to study a variety of plankton types, including laboratory cultures and natural micro-plankton communities.
5. **High-throughput**: The PlanktoScope is capable of high-throughput quantitative imaging, allowing users to analyze large numbers of samples quickly and efficiently.
6. **WiFi-enabled**: The PlanktoScope can be controlled from any WiFi-enabled device, making it easy to use and deploy in a variety of settings.
7. **Portable**: The PlanktoScope is small and portable, making it easy to transport and use in the field.
8. **Ease of use**: The PlanktoScope is designed to be easy to use, with instructions for assembly and use available on the PlanktoScope website.
## How do I get one?
You can access the complete [documentation](https://planktoscope.curious.bio/).
|Get the kit|Assemble your kit|Start your machine|
|--|--|--|
|![Get the kit](docs/images/readme/get_kit.png)|![Assemble your kit](docs/images/readme/assemble_kit.png)|![Start your machine](docs/images/readme/start_pscope.png)|
## Getting Involved
There are several ways you can join the development effort and contribute to this project.
### Communication Platform
We use Slack as a communication platform for interested parties. You can request to join by filling out [this form](https://docs.google.com/forms/d/e/1FAIpQLSfcod-avpzWVmWj42_hW1v2mMSHm0DAGXHxVECFig2dnKHxGQ/viewform).
### Reporting Issues
If you have identified a bug in the software or hardware, please open an issue in this repository to report it.
### Contributing to Development
You can also contribute to the development effort by working on open issues. Check out the [issues labeled as good first issues](https://github.com/PlanktoScope/PlanktoScope/labels/good%20first%20issue) and let us know in the comments if you are interested in working on one. We may be able to provide guidance as you get started with the code.
## License Information
This repository contains various types of materials that are covered by different licenses. Please read the following information carefully to determine which license applies to the materials you wish to use.
### Hardware Files
All hardware files and documentation located in the `hardware` directory are released under the [CERN-OHL-S-2.0](https://ohwr.org/cern_ohl_s_v2.txt) license.
### Software Source Code
The source code located in the `flows` and `scripts` directories is released under the [GPL-3.0](https://www.gnu.org/licenses/gpl-3.0.en.html) license.
### Other Materials
All other materials, including documentation and pictures, are released under the [Creative Commons CC-BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) license.
If you wish to use any of the materials in this repository for a project that cannot be open-sourced, please contact us using Slack so we can discuss potential solutions.
We encourage you to fork this repository and publish any improvements you make. Doing so helps others and allows us to potentially integrate your changes into this repository.
Documentation for the production and usage of a
Prototype microscope for environmental monitoring

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# Changelog
## Image changelog
### V2.2.1: released 2021-05-11
Bugfix:
- Package update to fix an issue were newer boards would not get recognised properly, leading to an early crash of the python script.
Improvement:
- Addition of a small menu to switch branches of the software. This is going to be of use mainly to developers.
**[Image download link](https://drive.google.com/file/d/1y0k_NDXN0yT5caZrXhjLYXgQVxu-D5ql/view?usp=sharing)**
### V2.2: released 2021-01-15
Breaking changes:
- new UI: more intuitive and more complete, with data validations checks and helpful tooltips
Improvements:
- Random camera crash solved: instead of using the python picamera library, we now use a compiled binary, `raspimjpeg` (whose source code is [here](https://github.com/PlanktonPlanet/userland/tree/master/host_applications/linux/apps/raspicam)). It's controlled through a FIFO pipe.
- Raspberry HQ camera support (the pixels are bigger (1,55µm vs 1,12µm on the camera v2.1) so with the same optics, the resolving power of your images is going to be reduced at 1µm per pixel vs 0,7µm per pixel with the 25mm/16mm lens couple).
- White balance control of the image
- Data backup on USB drive: all the files contained in `/home/pi/data` are copied over to your usb key
- Integrity check of the generated files (for now only for raw pictures and `metadata.json`. A file called `integrity.check` is created alongside the images. This file contains one line per file, with the filename, its size and a checksum of both its filename and its content.
- Gallery: allows you to browse the data folder to see the images you captured and the segmentation results.
- Update mechanism: for now, this only updates the code of the PlanktoScope and not the underlying OS.
- Wifi configuration tab: you can configure the Wifi network you want the machine to connect to.
- Hardware configuration tab: to customize the settings dependind on the hardware you use, (pump steps per mL, stepper driver type).
Probably broken:
- Embedded segmentation: it's been a while since we touched it. It should still be working, but you may experience bugs with it... If that's the case, please come forward so we can help solve those before the next release!
**[Image download link](https://drive.google.com/file/d/1fht8r7P6_bVsfIIwo7wnGLQ_1uxWCnos/view?usp=sharing)**
### V2.1: released 2020-10-14
Breaking changes firsts:
- There is no GUI on this image, it was created based on the Raspberry OS Lite, so no GUI. A new non-lite version is expected for late next week.
- The wifi network is now named `PlanktoScope`, and the password to it is `copepode`.
- The default user is `pi` and the default password is `copepode` for this user.
- The images captured and the segmentation output is now in the folder `/home/pi/data`
Improvements:
- Under the hood, whole new code is running! There is still a small bug that is triggered when running long imaging sequences, if this happens, restart the machine! We are working on finding where the problem may comes from. This bug is chased here.
- Another change: automatic wifi setup! If you setup your Raspberry to connect to a wifi network (by configuring wpa_supplicant.conf) it will try to connect to this network before starting its hotspot. Also, if you connect it to a wired network via its Ethernet port, it will share this connection to devices connected to the hotspot!
- The documentation has been updated to include more information about the ribbon assembly and how to create a backup of your sd card!
**[Image download link](https://drive.google.com/file/d/1zOmbmXqt5uELQC0FTha1ndjJyMvehGSk/view?usp=sharing)**

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# Contributor Covenant Code of Conduct
## Our Pledge
We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.
## Our Standards
Examples of behavior that contributes to a positive environment for our
community include:
* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the overall
community
Examples of unacceptable behavior include:
* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting
## Enforcement Responsibilities
Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.
Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.
## Scope
This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at
[INSERT CONTACT METHOD].
All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the
reporter of any incident.
## Enforcement Guidelines
Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:
### 1. Correction
**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.
**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.
### 2. Warning
**Community Impact**: A violation through a single incident or series of
actions.
**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.
### 3. Temporary Ban
**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.
**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.
### 4. Permanent Ban
**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.
**Consequence**: A permanent ban from any sort of public interaction within the
community.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
[https://www.contributor-covenant.org/translations][translations].
[homepage]: https://www.contributor-covenant.org
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations

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# Getting in touch with the community
PlanktoScope is a completely open platform. The core of the PlanktoScope project is a basis in an evolving network of designers and users collaborating to increase the impact and availability of the tools. Building a community of users will enable PlanktoScope to grow with capabilities not yet imagined.
For around $800, and with parts freely available in most parts of the globe, any person with the desire to engage can begin building a PlanktoScope. This website contains the information needed to assemble, test, and begin collecting data on your PlanktoScope.
## Engage on GitHub
Feel free to visit the **[GitHub](https://github.com/PlanktoScope/PlanktoScope)** and engage if you want.
<a href="https://github.com/PlanktoScope/PlanktoScope" rel="GitHub">![GitHub](../images/community/github.png)</a>
GitHub is a web-based platform that is widely used in the PlanktoScope Community for version control and collaboration. It allows members to easily share, track, and manage code and other project files. The platform is built around the Git version control system, which allows multiple contributors to work on the same codebase simultaneously while keeping a record of every change made.
In the PlanktoScope Community, members can use GitHub to collaborate on the development of the Planktoscope project. They created a central repository where they can share and track the code, documentation, and other project files.
## Chat on Slack
The community is using **[Slack](https://planktoscope.slack.com)** to communicate.
<a href="https://planktoscope.slack.com" rel="Slack">![Slack](../images/community/slack.png)</a>
Slack is a communication and collaboration tool that is widely used in the PlanktoScope Community. It allows members to communicate and work together in real-time, providing a central hub for all conversations related to Planktoscope project. The platform offers features such as direct messaging, group channels, video conferencing, and file sharing, making it easy for members to stay informed and on the same page.
The PlanktoScope community has created a dedicated Slack workspace for the community members to share their findings, ask for help, and discuss project-related topics.
## Classify on EcoTaxa
To join **[EcoTaxa](https://ecotaxa.obs-vlfr.fr/register)**, you just need to create an account.
<a href="https://ecotaxa.obs-vlfr.fr/register" rel="EcoTaxa">![EcoTaxa](../images/community/ecotaxa.png)</a>
EcoTaxa is a web-based platform that enables researchers, educators, and citizen scientists to identify, classify and share images of microorganisms. The platform is designed to support biodiversity research and education by providing a user-friendly interface for browsing and analyzing images of microorganisms, as well as a collaborative environment for sharing images and data. EcoTaxa allows users to upload their own images, and the platform's machine learning algorithms can automatically identify and classify the organisms in the images.
The platform also offers a variety of tools for analyzing and visualizing data, including image annotation, statistical analysis, and data export. Additionally, EcoTaxa has a community feature where researchers can share their findings, and have a discussion on the data, and contribute to the knowledge base. Overall, EcoTaxa is a valuable resource for anyone interested in microorganism biodiversity research and education.

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# Trainings
The success of the PlanktoScope community depends on the people who generously share their knowledge and expertise about its production and use with others, helping to promote its widespread adoption and use. By actively participating in the community and sharing their insights and experiences, individuals can contribute to the growth and success of the PlanktoScope, ultimately benefiting not just the community but also the broader field of study.
## The Train the trainer program
The train the trainer program is a training program designed to equip individuals with the knowledge and skills needed to deliver training to others. The goal of a train the trainer program is to build capacity within the PlanktoScope community by volunteers to become trainers themselves.
This guide is intended to provide you with a solid foundation of knowledge and understanding about the PlanktoScope, enabling you to confidently develop and deliver your own training program for others. Whether you are an experienced user looking to share your expertise with others or a newcomer to the PlanktoScope looking to learn more about its capabilities and applications, this guide is designed to help you gain the necessary skills and knowledge to successfully teach others about this powerful tool.
## Event types
### Build workshop
Organizing a build workshop can be a challenging but rewarding experience. It requires careful planning and execution to ensure that the workshop is successful. This trainer manual is designed to guide you through the process of organizing a build workshop.
#### Selecting the production site
Choosing the right production site for preparing and manufacturing the PlanktoScope Kits is an important step in the workshop planning process. The production site should have the necessary tools and equipment, as well as the knowledge and expertise to manufacture the PlanktoScope Kits. Here are a few things to consider when choosing a production site:
1. **Check the Manufacturing and Assembly Guides**: Before choosing a production site, make sure to review the PlanktoScope [Manufacturing Guide](/hardware/manufacturing/) and the [Assembly Guide](/hardware/assembly_guide/). These guides will provide detailed information on the necessary tools and equipment required for the production of the PlanktoScope Kits.
1. **Visit [Fablab](https://fablabs.io/labs) and [Hackspaces](https://wiki.hackerspaces.org/List_of_Hacker_Spaces)**: Consider visiting Fablabs or Hackspaces in your region. These organizations often have a culture of openness and may be willing to support you with your project. They may have the necessary tools and equipment to produce the PlanktoScope Kits, as well as the knowledge and expertise to guide you through the production process.
1. **Commercial Manufacturing**: Look for a facility that has the capability to handle small scale production runs, a good quality control process and a logistic plan to ship the product to the final destination. Many
!!! tip
For the PlanktoScope case, for example, you can look for woodworking companies. They often have a CNC machine and are familiar with the process of ditigal production.
#### Material procurement
Building a PlanktoScope requires a specific set of materials. In order to ensure that the workshop runs smoothly and that all attendees are able to successfully build their own PlanktoScope, it is important to properly plan and execute the procurement of materials. The following is a step-by-step guide on how to properly plan and execute the procurement of materials for a workshop:
1. **Prepare the order list**: Use the bill of materials (BOM) as a starting point to create a comprehensive list of all materials needed for the workshop. Expand it with additional columns for suppliers, delivery dates, prices, shipping costs, and import taxes.
2. **Plan for packaging**: Plan for extra packaging so you can assemble the parts as shown in the instructions. Try to minimize plastic as much as possible.
3. **Research suppliers**: Research suppliers and see if there are local options, if you can consolidate orders to save costs and ensure timely delivery.
4. **Compare prices**: Compare the prices of different suppliers to minimize the total cost.
5. **Plan for spare parts**: Plan for spare parts in case something is broken or lost.
6. **Check your Budget**: Check your budget and ensure that you have enough funds to cover the cost of all materials, shipping, and any additional expenses before placing your orders.
7. **Place orders**: Once you have identified the best suppliers, place orders for all of the materials that you need. Be sure to factor in lead time when placing orders to ensure that the materials will arrive in time for the workshop.
8. **Track orders**: Keep track of your orders and expected delivery dates, mark a component when it arrives. Contact suppliers if there are any delays or problems with delivery.
9. **Communicate**: Communicate with participants if there are issues with timely delivery. It may make sense to postpone the workshop if there is not enough time to prepare and test everything. The participants will be grateful and will understand if it helps to ensure that everything runs smoothly.
By following this process, you can ensure that all materials are procured and organized well in advance of the workshop, to avoid any last-minute delays or complications.
!!! note
If you have difficulty finding the components you need, [contact us](https://planktoscope.slack.com/) and we will be happy to help you find the right alternative.
!!! warning
Have a backup plan and be prepared for unexpected events that may occur during the procurement process. Allow two months for delivery, as some specialty parts may travel a long way and require additional time for customs inspection.
!!! tip
Let us know your results, we would love to hear what solutions you found and how cost effective you were able to make the PlanktoScope.
#### Prepare the Kit
Kit preparation for the workshop is an important step in the preparation process. This ensures that participants have the materials and equipment they need to complete the workshop and build their own PlanktoScope. Here are a few things to keep in mind when preparing the kits:
1. **Review the Bill of Materials (BOM)**: Review the Bill of Materials (BOM) for the PlanktoScope to ensure that you have all the necessary parts and materials for the workshop. The parts list can be found in the [Assembly Guide](/hardware/assembly_guide/) and lists all components and quantities needed to build a microscope.
2. **Divide the kit components according to the BOM**: Once the materials have been received, divide the kit components from the orders according to the Bill of Materials (BOM) of the PlanktoScope. This will ensure that each participant receives the correct components and that there are no missing parts.
3. **Have extra components**: Have extra components on hand in case of any missing or damaged parts during the workshop.
4. **Package the kits**: Package the kits in a way that makes it easy for the participants to find and use the components during the workshop.
5. **Label materials**: Label the packages as described in [Assembly Guide](/hardware/assembly_guide/) so that they are easy to find and distribute during the workshop.
6. **Preparation of the housing parts**: Prepare the housing parts by applying the surface sealant and insert the nuts to screw the housing as described in the [Manufacturing Guide](/hardware/manufacturing/#finishing).
7. **Cutting and soldering of electronic cables**: Cut and solder the electronic cables for the PlanktoScope. This will save time during the workshop and ensure that the participants have all the necessary cables to complete the assembly.
8. **Setting up the embedded development environment**: Set up the embedded development environment and flash the eeprom of the PlanktoScope hat. This will ensure that the PlanktoScope hat is ready to be used during the workshop.
9. **Download the Raspberry Pi image**: Download the Raspberry Pi image and flash it to the SD card. This will ensure that the participants have a ready to use image for the PlanktoScope.
10. **Test the kits**: Test the kits before the workshop to ensure that all components are working correctly and that the instructions are clear and easy to follow. This will help to ensure that the participants have a positive and productive experience during the workshop.
!!! tip
Identify any items that are time consuming during the workshop and not particularly important or complex to explain. These tasks can be completed in advance to save time during the workshop. This will make it easier for the participants to assemble the PlanktoScope during the workshop.
#### Conducting the workshop
It's finally here! After all the planning, preparation, and anticipation, the build workshop is about to begin. Take a deep breath and let's go!
1. **Prepare the presentation**: Prepare the presentation device and start your slides.
2. **Check-In**: Once the Participants arrive, complete the check-in, share the agenda and set expectations for the workshop.
3. **Venue**: Provide information about the venue, including where to find restrooms and where to buy food.
4. **Digital tools**: Provide information about the digital tools that will be used during the workshop, such as the platform for collaboration, the survey tool and the chat channel, and how to access them.
5. **Data privacy**: Inform about the privacy policy and the forms that need to be signed by the participants if you want to take photos.
6. **Introduction round**: Begin with a round of introductions and give everyone a chance to introduce themselves, their background, and their interest in the project.
7. **Provide an overview**: Provide details about the project, including the general mode of operation, the working materials such as the kit, the documentation and the git repository.
8. **Provide the Kits and Tools**: Provide the Kit and Tools to each participant with a kit and the necessary tools.
9. **Follow the build instructions**: Depending on the format you have chosen, start implementing by following the [Manufacturing guide](/hardware/assembly_guide/) or [Assembly guide](/hardware/manufacturing/)
10. **Follow the usage instructions**: Now that you have successfully assembled the PlanktoScope, you can proceed to the usage by following the [Getting started](/usage/getting_started/) and [User interface](/usage/ui_guide/) instructions.
11. **Final Test**: For a final test you can use for example pure cultures or a sample taken with a [PlanktonNet](/hardware/accessories/#plankton-net) from a surrounding waters.
### Field trip
Are you an expert in organizing field trips? Share your skills with the PlanktoScope community by documenting the process! By documenting how you organize a field trip, you can help others create successful events and bring more event options to the PlanktoScope community. Your documentation will be a valuable resource for anyone looking to plan a field trip, and it will also help to grow and strengthen the PlanktoScope community. Don't miss this opportunity to contribute to the community, start documenting your process today!
### Hackathon
Are you a master at organizing Hackathons? Share your knowledge with the PlanktoScope community by documenting the process! By documenting how you organize a Hackathon, you can help others create successful events and bring more event options to the PlanktoScope community. Your documentation will be a valuable resource for anyone looking to host a Hackathon, and it will also help to grow and strengthen the PlanktoScope community. Don't miss this opportunity to contribute to the community, start documenting your process today!
## General planning methods
Organizing a workshop can be a challenging but rewarding experience. It requires careful planning and execution to ensure that the workshop is successful. This trainer module is designed to guide you through the process of organizing any type of event.
By following the guidelines, you will be able to plan a workshop that is engaging, productive, and successful. It will also help you to create a sense of community among participants and will help them continue their learning after the workshop.
### Building a team
Every project needs a team to support it. The team should be composed of individuals with a diverse set of skills and experiences to ensure all aspects of the workshop are effectively covered.
1. **Identify the roles and responsibilities**: Determine the key areas that need to be covered during the workshop and assign specific roles to team members. For example, one team member may be responsible for organizing logistics, while another may be responsible for creating the agenda.
2. **Assemble the team**: Once the roles and responsibilities have been identified, begin assembling the team. Consider individuals with relevant skills and experiences, as well as those who have a passion for the topic of the workshop. It is also important to have a mix of team members from different departments or backgrounds to bring a variety of perspectives to the planning process.
3. **Communicate effectively**: Establish clear lines of communication within the team to ensure that everyone is on the same page. This can be done through regular meetings, email, or a team collaboration platform.
4. **Encourage participation**: Encourage team members to actively participate in the planning process by sharing their ideas and feedback. This will help to ensure that everyone feels invested in the success of the workshop.
5. **Appoint a leader**: Appoint a leader for the team who will be responsible for coordinating the planning process and ensuring that the team stays on track. The leader should be someone who is organized, a good communicator, and able to delegate tasks effectively.
### Communication channels
Choosing the right communication channels is an important step in the planning process for a workshop, as it is crucial not only for the organizing team but also for the participants during and after the workshop. The right communication channels can help to build a fluent community, improve collaboration and keep everyone informed and on the same page.
1. **Choose the right channels**: Once the needs have been identified, choose the communication channels that will best serve those needs. Email, chat, and video conferencing are all popular options. If the group is small, a group chat or email chain may be sufficient. If the group is larger or more dispersed, a video conferencing platform may be more appropriate.
2. **Make sure they are accessible**: Ensure that the communication channels you choose are accessible to all participants. This may include providing training or support for those who are less familiar with the tools you are using.
3. **Communicate expectations**: Clearly communicate the expectations for using the communication channels to the participants. This includes guidelines for how often and when to check the channels, as well as how to respond to messages.
4. **Continuity**: Make sure that you have continuity in the communication channels after the workshop. This will help to build a fluent community and to keep the participants connected and engaged. Use the same channels to share updates and resources, or to organize follow-up events or activities.
!!! note
Email is a reliable and widely-used communication channel that can be used for sending out workshop updates, sending materials, and answering questions. It is also a good option for sending out reminders and follow-up information after the workshop.
!!! note
Chat networks, such as [Matrix](https://matrix.org/), are a great option for secure, real-time and decentralized communication during the workshop. They allow participants to ask questions, share resources and collaborate on projects in real-time. They can also be used for group discussions and as a platform for sharing feedback. Additionally, chat platforms can be used as a platform for post-workshop communication and to build a fluent community.
!!! tip
If you need assistance with creating a Chat for your workshop, please let us know. We can easily set up new subchannels within our [PlanktoScope Slack channel](https://planktoscope.slack.com/) to support communication and collaboration during your workshop. This will also help facilitate the exchange of information within the community.
### Selecting digital tools
The right tools can help to facilitate communication, collaboration, and organization, making the workshop experience more productive and enjoyable for everyone.
1. **Use web-based tools**: Whenever possible, use web-based tools that can be accessed from any device with an internet connection. This will make it easier for participants to access and use the tools, regardless of their location or device.
2. **Use collaborative note-taking tools**: You might use web-based tools like [HedgeDoc](https://hedgedoc.org/) that allow participants to collaboratively collect notes during the workshop. This can help to ensure that everyone has access to the same information, and can help to make the workshop experience more productive and enjoyable for everyone.
3. **Use survey tools**: You might use survey tools like [LimeSurvey](https://www.limesurvey.org/) to gather information about the participants' needs and expectations for the workshop. This can help to ensure that the workshop is relevant, valuable, and effective for them.
4. **Use ticketing tools**: You might use tools like [Pretix](https://pretix.eu/) to manage ticketing for the workshop. This can help to simplify the registration process, and can also provide valuable information about the attendees.
### Find your audience
If you already have an audience for your workshop, that's fantastic. But it's also a good idea to let others know about your plans and potentially expand your audience. Contact nongovernmental organizations, universities, and research institutions in your area to see if they would be interested in participating in or even helping to organize the workshop.
!!! tip
One way to get in touch with others who are interested in PlanktoScope is to join our [Slack Channel](https://planktoscope.slack.com/). We can support you by sharing contacts of individuals and organizations who have expressed an interest in PlanktoScope.
### Determining the need
Understanding the needs of the participants will help to ensure that the workshop is relevant, valuable, and effective for them. Here are a few things to consider when determining the needs of the participants:
1. **Surveys and questionnaires**: Use surveys and questionnaires to gather information about the participants' needs and expectations for the workshop. This can include their level of experience and knowledge, their specific interests and goals, and any challenges or concerns they may have.
2. **Pre-workshop consultation**: Schedule pre-workshop consultations with the participants to discuss their needs and expectations in more detail. This can help to identify any specific areas of interest or concern, and can also provide an opportunity to address any questions or concerns the participants may have.
3. **Audience analysis**: Analyze the characteristics of the audience, such as their profession, level of education and experience, and any other relevant details. This will give you a better idea of the type of content that will be most relevant and useful for the participants.
4. **Feedback**: Ask for feedback from participants after the workshop and take it into account when planning future workshops. This feedback can be used to improve the overall experience and to tailor the workshop to better meet the needs of the participants.
### Defining the goals
Defining the goals of a workshop is an essential step in the planning process. The goals will serve as the foundation for the workshop, guiding the content and activities that are included.
1. **Number of participants**: The workshop should be designed for a specific number of participants. Depending on the available resources, the number of participants can range from small groups of 4-8 people to larger groups of 8-12 people.
1. **Number of microscopes**: The goal of the workshop is to build a specific number of PlanktoScope Microscopes. It is important to have the necessary materials and tools for each participant to build their own microscope.
1. **Content**: The workshop will include both theoretical and practical content. The theoretical content will cover the principles of open-source hardware and software and the specific design of the PlanktoScope Microscope. The practical content will focus on the assembly and usage of the microscope, including hands-on experience with soldering and other techniques.
!!! tip
Depending on the time, resources, and audience, it is important to carefully decide what activities and tasks should be done during the workshop and what should be prepared upfront. This will ensure that the workshop runs smoothly and efficiently, and that the participants are able to fully engage and participate in the activities. Additionally, by carefully planning and preparing upfront, you can minimize the chances of overwhelming attendees with problems or difficulties that may arise during the workshop.
### Financial planning
The cost of materials, equipment, and other expenses can add up quickly, so it is important to have a plan in place to secure funding. Here are a few things to consider when planning the finances for your workshop:
1. **Decide on the cost of the kits**: One of the first things to consider is whether you want to offer the kits for sale to the participants or if you want them to purchase the kits themselves. If you choose to offer the kits for sale, you will need to factor in the cost of materials and other expenses, such as shipping and handling. If you choose to have the participants purchase the kits themselves, you will need to provide them with information on where to purchase the kits and the estimated cost.
2. **Check for funding opportunities**: There may be organizations or foundations that would be willing to support your workshop financially. It's a good idea to research potential sources of funding such as grants, sponsorships, and crowdfunding campaigns. Additionally, look for local or regional organizations that are working in the same field as your workshop, they might be interested in supporting your initiative.
3. **Reach out to potential sponsors**: Once you have identified potential sources of funding, reach out to them to inquire about their funding opportunities. Be prepared to provide them with information about the workshop, including the goals, objectives, and expected outcomes. Be sure to include information about the open-source nature of the project, as this may make it more attractive to organizations with an interest in open-source technology.
4. **Look for cost-saving options**: In addition to securing funding, there are also ways to save money on expenses. Consider renting equipment or space rather than purchasing it. Reach out to local universities or community organizations to see if they have equipment or space that you can use for the workshop at a reduced cost or for free.
!!! tip
If you are organizing the workshop as an individual, consider running the project through a non-profit organization to facilitate the collection of donations. This will also help to ensure transparency and accountability for the funding received. Alternatively, you can choose a commercially active organization that can provide proper accounting and financial management for the workshop participants. This will provide a clear financial record and can help to ensure that the workshop is run in a professional and organized manner.
### Creating a timetable
Creating a schedule for a workshop is an important step in the planning process. A well-organized schedule will help to ensure that the workshop runs smoothly and that all the important topics are covered. Here are a few things to consider when creating a schedule for your workshop:
1. **Plan for more than just a day**: A workshop may take more than one day to complete, so be sure to plan accordingly. Consider the amount of time required to cover all the topics, and allocate enough time for each one.
1. **Assign an expected duration to each item on the schedule**: Assign an expected duration to each item on the schedule so that participants know how much time they should expect to spend on each topic. This will also help you to ensure that you have allocated enough time for each topic.
1. **Allocate time for breaks and activities**: Make sure to allocate time for breaks, meals and other activities such as group discussions, teamwork, or hands-on activities. This will help to keep the participants engaged and energized throughout the workshop.
1. **Plan for contingencies**: Include some flexibility in the schedule to allow for unexpected events or delays. This will help to ensure that the workshop stays on track even if things don't go exactly as planned.
### Venue selection
The location should be convenient and accessible for the participants, and should be equipped with the necessary resources to make the workshop a success. Here are a few things to consider when choosing a workshop location for a workshop on building an open-source PlanktoScope microscope:
1. **Reach out to Universities, research institutions, Fablabs, Hackspaces or non-profit organizations**: Reach out to organizations that might have an interest in the PlanktoScope, and a community that might support you with free access to their location.
2. **Check the equipment**: Make sure the location is equipped with the necessary resources such as a whiteboard, projector/TV, and other equipment that may be required for the workshop.
3. **Check the accessibility**: Check the accessibility of the location with the public transport system and parking availability.
4. **Check for food provision**: Consider if there is a possibility to go shopping or how to provide food for the course participants during the workshop.
5. **Check the environment**: Consider the environment of the location, make sure it is comfortable, has enough space and is well-ventilated for the workshop.
### Announcing the event
When announcing the event, it is important to include the following information:
1. **Date**: Provide a specific date, start and end time for the workshop, and ensure there is enough lead time for preparation, including ordering or manufacturing materials and coordinating with suppliers. Allow ample time between announcing the workshop and the actual event.
2. **Goal**: Clearly communicate the specific goal of the workshop, such as to build a fully functional planktoscope and learn how to use it.
3. **What attendees will learn in the workshop**: Clearly outline the specific skills or knowledge that will be covered in the workshop, such as how to assemble the kit, soldering the through-hole components of the controller, and working with the software.
4. **Instructor's background**: Provide some notes about the instructor's qualifications or experience that make them well-suited to lead the workshop, such as experience working with planktoscope.
5. **Target audience**: Clearly indicate the target group of the workshop, such as researchers, engineers or designers.
6. **Previous knowledge**: Specify any previous knowledge required for the workshop, such as soldering skills or experience working with open-source hardware and software.
7. **Implementation method**: Describe the form of the workshop, such as a step-by-step guide.
8. **Documentation**: Consider sharing the documentation beforehand, so they can familiarize themselves with the process.
9. **Cost**: Clearly communicate the cost of the workshop.
10. **Schedule**: Provide a clear and detailed schedule of the workshop, including the duration of the workshop, for example, one day of building and one day of using the plankoscope.
11. **Location**: Provide the location of the workshop, including information on how to get there with public transportation or Arrival by car and parking. Also, provide a link to a map service
12. **Registration**: Details of the registration process, including information on where to obtain a ticket and any deadlines for registration.
13. **Contact details**: Additionally, it may be helpful to include contact information for any questions.
14. **Images**: Include some visually appealing images, such as from a previous workshop or field trip, to show what attendees can expect from the event. This can additionally be a great way to build anticipation and excitement, thus motivating more people to attend the workshop.
15. **Media**: Post your offer on a website or social media platform that is relevant to the workshop topic and your target audience. This way you can increase visibility and reach a wider audience, which increases the chances of getting more attendees.
!!! tip
If you already have a group of interested people, send a link to the announcement via email or chat and invite them personally.
### Preparing a presentation
Preparing a presentation for a build workshop is an important step in the preparation process. It helps to ensure that the participants have the information they need to complete the workshop and understand the concepts behind building the Planktoscope.
1. **Gather resources**: Gather resources such as images, videos, and diagrams that can be used to support the presentation. These resources can be found on the Planktoscope website or other sources.
2. **Outline the main topics**: Outline the main topics that will be covered during the workshop, such as the components of the microscope, the assembly process, and the use of the microscope.
3. **Prepare a handout**: Prepare a handout or a guide that the participants can use during the workshop to follow the steps, and have it ready to be printed or shared digitally
4. **Practice the presentation**: Practice the presentation several times before the workshop to ensure that it runs smoothly and that you are comfortable with the material.
5. **Be ready to adapt**: Be ready to adapt the presentation during the workshop to fit the needs of the participants.
Here are some topics that should be covered in a presentation:
1. **Event**: Provide an overview of the event, including the goal of the workshop.
2. **Schedule**: Provide an timetable for the event, including breaks, start and end times, and any planned activities for the next day.
3. **Venue**: Provide information about the venue, including where to find restrooms and where to buy food.
4. **Instructor**: Provide information about the instructor, including his or her background, and how to get in touch with him or her
5. **Digital tools**: Provide information about the digital tools that will be used during the workshop, such as the platform for collaboration, the survey tool and the chat channel, and how to access them
6. **Data privacy**: Provide information about the data privacy policy and the forms that need to be signed by the participants.
7. **Follow-ups**: Point out follow-up actions such as the survey and that participation can be very helpful in improving the offer.
8. **Communication**: Inform about the communication channels that will be used during the workshop and complete the onboarding.
9. **Introduction round**: A round of introductions at the beginning of a workshop helps to create a sense of community and connection among the participants, allows the instructor to tailor the workshop to the group's needs, addresses potential language barriers, creates a sense of accountability, and helps participants to be more focused and relaxed.
10. **About the project**: Provide details about the project, including the working materials such as the kit, the documentation, and the git repository.
### Send an final Reminder
Make sure participants are well informed and can find their way to you by sending a final reminder before the start so everything is well prepared.
1. **Schedule for the event**: Include a detailed schedule for the event, including breaks, start and end times, and any planned activities for the next day. This will help participants to plan their time and make the most of the workshop.
2. **About the venue**: Provide detailed information about the venue, including the address, public transportation options, and parking situation. Make sure to include any specific instructions or requirements for accessing the venue.
3. **About the documentation**: Provide a link to the documentation, such as the assembly and manufacturing guide, that the participants can familiarize themselves with before the workshop. This will help them to be better prepared and make the most of the workshop.
4. **Cancellation policy**: Remind the participants that now is the last opportunity to cancel their registration. This will allow other individuals on the waiting list to attend the workshop.
5. **Final Instructions**: Provide any final instructions or important information that the participants should be aware of before the workshop.
### Documenting the event
Documenting a PlanktoScope workshop through photography is essential for several reasons. Photos can be used to showcase the workshop activities and the learning process of the participants. This can be useful for sharing information about the workshop with others, and for promoting future workshops.
1. **Equipment**: Make sure you have the necessary equipment to document the event, including a camera (DSLR or mirrorless camera), lenses, memory cards, and batteries.
2. **Backup**: Always make sure to have a backup plan for your equipment and photos, such as bringing extra memory cards and batteries.
3. **Lighting**: Take into account the lighting conditions and make sure to have the right settings for your camera to capture the best possible images.
4. **Planning**: Plan out the photos you want to take, taking into account the theme, location and schedule of the event.
5. **Composition**: Pay attention to the composition of your photos and make sure to use techniques such as the rule of thirds and leading lines to create visually appealing images.
6. **Capturing candid moments**: In addition to capturing posed shots, make sure to capture candid moments that capture the atmosphere and emotions of the event.
7. **Post-processing**: Once the event is over, review and edit your photos to make them look their best.
8. **Data Privacy and Opt-Out**: Pay attention to the privacy policy and get participants' consent before taking photos of them. Offer an opt-out option for participants who do not want to have photos taken. Clearly communicate what the photos will be used for and by whom, for example, to enhance this documentation.
9. **License**: If your participants have agreed to share and use the photos, choose an appropriate license under which to license the photos. We recommend the [Creative Commons license](https://creativecommons.org/). For more information, see the [project's license terms page](/license/).
10. **Sharing on Social Media**: Share the photos on social media platforms to create a visual memory of the event and increase the visibility of the event.
By preparing and taking care of these things, you can ensure that you are able to document the event effectively and create a visual record of the event that can be shared and enjoyed for years to come.
### Follow-up
Follow-up activities are an essential part of the workshop planning process. They help to ensure that the workshop's objectives are met and that the participants leave the workshop with a sense of accomplishment. Here are a few things to consider when planning follow-up activities after an event like a workshop:
1. **Follow-up with participants**: Send out a survey or contact participants individually to gather feedback on their experience during the workshop. This feedback can be used to improve future workshops and address any issues that may have arisen.
2. **Share resources and information**: Share any relevant resources such as presentations, handouts, or any other materials that will help the participants continue their learning after the workshop.
3. **Build a community**: Encourage participants to connect and share their experiences with each other. This can be done through online forums, social media groups, or other platforms. Building a community of enthusiasts and collaborators will help to ensure that the workshop's goals and objectives are met and that the participants leave the workshop with a sense of accomplishment.
4. **Continual learning**: Provide additional training opportunities or resources for participants to continue their learning after the workshop. This could be through follow-up workshops, webinars, or online tutorials.
5. **Track progress**: Keep track of the progress of the participants, check if they are applying what they learned during the workshop and give feedback to help them improve.
## Improve this training program
As with any training program, there is always room for improvement. To ensure that this program continues to meet the needs of its attendees, it is important to actively seek feedback and make changes as necessary.
Here are a few ways to improve this training program:
1. **Gather feedback**: Regularly gather feedback from attendees, instructors and other stakeholders to understand how the program is being received and identify areas for improvement.
1. **Review and revise content**: Review the content of the program and make changes as necessary to ensure that it is up-to-date, accurate, and relevant to the attendees.
1. **Continuously update the material**: Continuously update the material, adding new information and best practices as it becomes available.
1. **Use different learning methods**: Use different learning methods to accommodate different learning styles, such as hands-on activities, group discussions, and online resources.
1. **Encourage participation**: Encourage participation and collaboration among attendees, creating an interactive and dynamic learning experience.
1. **Use modern technologies**: Use modern technologies to enhance the learning experience, such as virtual reality, gamification, and AI-based learning.
1. **Assess the impact**: Assess the impact of the program on the attendees and make changes as necessary to ensure that the program is achieving its intended goals.
For more information on how to contribute to this document and improve this training program, please see the [contribute section on Writing Documentation](/contribute/writing_documentation/).

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# User Group Directory
A PlanktoScope User Group is a place where you can go to hang out to learn about and use PlanktoScope. Typically this includes physical in-person meetups that happen regularly.
## Locations
### Germany
#### Hamburg
##### Curious Community Labs e.V.
| | |
| --------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
| **Location** | [Stockmeyerstraße 41, Halle 4K, 20457 Hamburg](https://www.openstreetmap.org/node/9615054340#map=19/53.54203/10.01036) |
| **Description** | The CCL is a self-organized and open biolab. It aims to provide infrastructure for do-it-yourself enthusiasts and a meeting place for tech and bio lovers. |
| **Website** | [curious.bio](https://curious.bio) |
| **Contacts** | [Sebastian Wendel](https://matrix.to/#/@swendel:curious.bio) |
| **Chat** | [#planktoscope:curious.bio](https://matrix.to/#/#planktoscope:curious.bio) |
| **Activities** | Organizing Workshops and realizing projects for Citizen-Science and Open-Hardware. Using the PlanktoScope for the analysis of biodiversity in peatlands. |
| **Hardware** | We have 12 devices. If you need one for a research project, ask us, we will be happy to lend you one. |
| **Meetups** | Every tuesday from 18:30, feel free to come by! |
## Add your place to this list
To add your place to the user group directory, you will need to edit [this file](https://code.curious.bio/curious.bio/planktoscope/src/docs/community/usergroups.md) by following a git pull request workflow outlined at [Github Workflow](/contribute/github_workflow/).

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# Contributing
First of all, thank you for contributing to the PlanktoScope! The goal of this document is to provide everything you need to know in order to contribute to PlanktoScope.
There are several ways to join the development effort, share your progress with your build or just ask for help.
We are using slack as a communication platform between interested parties. You can [request to join by filling this form](https://docs.google.com/forms/d/e/1FAIpQLSfcod-avpzWVmWj42_hW1v2mMSHm0DAGXHxVECFig2dnKHxGQ/viewform).
This repository is also a good way to get involved. Please fill in an issue if you witnessed a bug in the software or hardware. If you are able, you can also join the development effort. Look through the [issues opened](https://github.com/PlanktonPlanet/PlanktoScope/labels/good%20first%20issue) and choose one that piques your interest. Let us know you want to work on it in the comments, we may even be able to guide your beginnings around the code.
- [Contributing](#contributing)
- [Assumptions](#assumptions)
- [How to Contribute](#how-to-contribute)
- [Development Workflow](#development-workflow)
- [Git Guidelines](#git-guidelines)
- [Release Process (for internal team only)](#release-process-for-internal-team-only)
## Assumptions
1. **You're familiar with [git](https://git-scm.com/) and the [Merge Request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)(PR) workflow.**
2. **You've read the PlanktoScope [documentation](https://planktonscope.readthedocs.io/) and the [images/readme](/images/readme.md).**
3. **You know about the PlanktoScope [community on Slack](https://planktoscope.slack.com/). Please use this for help.**
## How to Contribute
1. Make sure that the contribution you want to make is explained or detailed in a GitHub issue! Find an [existing issue](https://github.com/PlanktoScope/PlanktoScope/issues) or [open a new one](https://github.com/PlanktoScope/PlanktoScope/issues/new/choose).
2. Once done, [fork the PlanktoScope repository](https://docs.github.com/en/get-started/quickstart/fork-a-repo) in your Github account. Ask a mastertainer if you want your issue to be checked before making a PR.
3. [Create a new Git branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository).
4. Review the [Development Workflow](#development-workflow) section that describes the steps to mastertain the repository.
5. Make the changes on your branch.
6. [Submit the branch as a PR](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) pointing to the `master` branch of the master fabcity-os-core-chart repository. A mastertainer should comment and/or review your Pull Request within a few days. Although depending on the circumstances, it may take longer. We do not enforce a naming convention for the PRs, but **please use something descriptive of your changes**, having in mind that the title of your PR will be automatically added to the next [release changelog](https://github.com/PlanktoScope/PlanktoScope/releases).
## Development Workflow
### Setup <!-- omit in toc -->
In order to use the different tools on this repository, you will first need to:
```sh
```
### Tests and Linter <!-- omit in toc -->
Each PR should pass the linter to be accepted.
```sh
make lint
```
Each PR should also check if the generated file `manifests/fcoscore.yaml` is updated with the new modifications.
You can generated the manifest with the command line:
```bash
helm template fcoscore . | grep -v 'helm.sh/chart:\|app.kubernetes.io/managed-by:' > manifests/PlanktoScope.yaml
```
Or just by comment the PR:
```txt
@PlanktoScope sync-manifest
```
Additionally, the CI will run a test to check if there are changes introduced to the charts. If changes were introduced, it will require you to update the Chart version.
## Git Guidelines
### Git Branches <!-- omit in toc -->
All changes must be made in a branch and submitted as PR.
We do not enforce any branch naming style, but please use something descriptive of your changes.
### Git Commits <!-- omit in toc -->
As minimal requirements, your commit message should:
- be capitalized
- not finish by a dot or any other punctuation character (!,?)
- start with a verb so that we can read your commit message this way: "This commit will ...", where "..." is the commit message.
e.g.: "Fix the home page button" or "Add more tests for create_index method"
We don't follow any other convention, but if you want to use one, we recommend [this one](https://chris.beams.io/posts/git-commit/).
### Pull Requests <!-- omit in toc -->
Some notes on PRs:
- [Convert your PR as a draft]() if your changes are a work in progress: no one will review it until you pass your PR as ready for review.<br>
The draft PR can be very useful if you want to show that you are working on something and make your work visible.
- The branch related to the PR must be **up-to-date with `master`** before merging. Fortunately, this project [integrates a bot]() to automatically enforce this requirement without the PR author having to do it manually.
- All PRs must be reviewed and approved by at least one mastertainer.
- The PR title should be accurate and descriptive of the changes. The title of the PR will be indeed automatically added to the next [release changelogs]().
## Release Process (for internal team only)
PlanktoScope tools follow the [Semantic Versioning Convention](https://semver.org/).
### Automation to Rebase and Merge the PRs <!-- omit in toc -->
This project integrates a bot that helps us manage pull requests merging.<br>
_[Read more about this]()._
### How to Publish the Release <!-- omit in toc -->
⚠️ Before doing anything, make sure you got through the guide about [Releasing an Integration]().
⚠️ Every PR that is merged to `master` introducing changes to the PlanktoScope needs to modify the file [``](), by increasing the version of the chart accordingly.
Every PR that is merged to `master` triggers the automated release process, as specified at [``](). A GitHub Action will be triggered and publish a new release on the GitHub repository [releases](). This will enable users to start using the new version of the chart immediately after publishing.
Thank you again for reading this through, we can not wait to begin to work with you if you made your way through this contributing guide ❤️
- pdfimages -all protocols/PlanktoScope\ -\ Setup\ and\ Sampling\ Guide\ VER3.pdf protocols/dumps/PlanktoScope_Setup_and_Sampling_Guide_VER3
sudo apt-get install pandoc texlive-latex-base texlive-fonts-recommended texlive-extra-utils texlive-latex-extra
sudo apt install poppler-utils

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# Hardware Development
![planktoscope_hero](../images/project_description/planktoscope_versions_01.png)
## PlanktoScope Case
![autodesk_fusion_360](../images/logos/autodesk_fusion_360.png){ align=right width="200"}
As a hardware engineer working on the PlanktoScope Case, you will be using Autodesk Fusion 360 for the development of the case design. Fusion 360 is a comprehensive computer-aided design (CAD) software that allows you to create and analyze complex 3D models, perform simulations and stress tests, and collaborate with team members in real-time.
To get started with the project, you will need to install a development environment on your computer. Here are the steps to follow:
* Download and install [Fusion 360 from the Autodesk website](https://www.autodesk.com/products/fusion-360/overview).
* Create a free Autodesk account and log in to Fusion 360.
* Join the PlanktoScope Case team in Fusion 360. This will give you access to all of the project files and allow you to collaborate with other team members.
* Familiarize yourself with the Fusion 360 interface and tools. There are many resources available online, including tutorials and user guides, to help you get up to speed.
* Start designing and testing your case components in Fusion 360. You can use the software to create 3D models, run simulations and stress tests, and collaborate with other team members in real-time.
By following these steps, you will be able to successfully install a development environment and participate in the PlanktoScope Case using Autodesk Fusion 360.
## PlanktoScope Hat
![autodesk_eagle](../images/logos/autodesk_eagle.png){ align=right width="200"}
As a hardware engineer working on the PlanktoScope Hat, you will be using [Autodesk Eagle](https://www.autodesk.de/products/eagle) to design and develop the electronic components of the hat. Autodesk Eagle is a powerful and widely used software platform for designing and laying out printed circuit boards (PCBs).
To participate in the project, you will need to install a development environment on your computer that includes Autodesk Eagle and any other necessary tools and libraries. Here are the steps you can follow to set up your development environment:
* Download and install Autodesk Eagle from the [official website]((https://www.autodesk.de/products/eagle)). Make sure to select the appropriate version for your operating system (Windows, Mac, or Linux).
* Follow the instructions provided by Autodesk to complete the installation process. This may involve entering a license key or activating the software through your Autodesk account.
* Once Autodesk Eagle is installed, you may need to install additional libraries or tools depending on the specific requirements of the PlanktoScope Hat. These may include libraries for communicating with specific hardware components, or tools for debugging and testing your designs.
* Once you have installed all the necessary tools and libraries, you should be ready to start working on the PlanktoScope Hat using Autodesk Eagle. You can begin by opening the project files and familiarizing yourself with the existing design, or by creating new designs as needed.
By following these steps, you can set up a development environment that allows you to contribute to the PlanktoScope Hat using Autodesk Eagle.

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# How to help development for the PlanktoScope code
We are using the [Github Flow approach](https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests) for our development efforts.
If you want to join us, have a look at the [currently opened issues](https://github.com/PlanktonPlanet/PlanktoScope/issues) and pick one where you feel like you can have an impact. Let us know you want to work it in the comments and get started.
For working on Node-Red, we recommend to install it directly on your development machine to allow for faster cycles of testing (and ease of use). But feel free to setup a Pi Zero as a portable and compact development environment! (One of us is using one configured as usb gadget to do so!)
If you don't know how to code, [the documentation could use your help](edit_this_doc)!
## Node-Red
[Node-Red](https://nodered.org/) is our main process. We use [the flow](https://nodered.org/docs/developing-flows/flow-structure) to manage our user interface through a dashboard instance.
![node-red](../images/logos/node-red.svg){ align=right width="100" }
As a software engineer, you may need to set up a Node-RED development environment on a Debian operating system. Node-RED is an open-source programming tool for wiring together hardware devices, APIs, and online services in new and interesting ways. It provides a visual, drag-and-drop interface for building applications, and can be used to develop a wide range of IoT, automation, and data processing projects.
To set up a Node-RED development environment on a Debian operating system, you will need to follow these steps:
1. Install Node.js: Node-RED requires Node.js to be installed on your system. You can install Node.js using the package manager by running the following command: `sudo apt-get install nodejs`
2. Install npm (Node Package Manager): npm is a package manager for Node.js that is used to install and manage Node-RED and its dependencies. You can install npm by running the following command: `sudo apt-get install npm`
3. Install Node-RED: Once Node.js and npm are installed, you can install Node-RED by running the following command: `sudo npm install -g --unsafe-perm node-red`
4. Start the Node-RED server: You can start the Node-RED server by running the following command: `node-red`
5. Access the Node-RED editor: You can access the Node-RED editor by opening a web browser and going to the URL <http://localhost:1880>.
By following these steps, you will be able to set up a Node-RED development environment on your Debian operating system and start building applications with the visual, drag-and-drop interface.
## Python
![python](../images/logos/python.svg){ width="200" }
The python code is separated in four main processes, each with a specific set of responsibilities:
- The main process controls all the others, starts everything up and cleans up on shutdown
- The stepper process manages the stepper movements.
- The imager process controls the camera and the streaming server via a state machine.
- The segmenter process manages the segmentation and its outputs.
Those processes all communicates together using MQTT and json messages. Each message is adressed to one topic. The high level topic controls which process receives the message. The details of each topic is at the end of this commit message. You can learn more about the [MQTT Messages here](mqtt_messages).
The code is architectured around 6 modules and about 10 classes. I encourage you to have a look at the files, they're pretty straightforward to understand.

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# Writing Documentation
The source files are in the main [github repository](https://www.github.com/PlanktonPlanet/PlanktoScope), in the `docs` folder.
They are simple [Markdown files](https://www.markdownguide.org/), that you can edit in any text editor of your choice.
The local development and test is made using [mkdocs](https://www.mkdocs.org/). This allows you to test your documentation changes for styling issues and see what it will look like once rendered.
```sh
hatch run docs:serve
```
After installing mkdocs, you can use `mkdocs serve` in the main folder of this repository to start the development server.
If you want to include pictures and diagrams in the documentation, please set the pictures in a dedicated folder to the name of the page you are creating (for example, if your page is named `expert_setup.md`, please put all the related pictures in the `docs/expert_setup/` folder). Each picture should be named with a simple yet descriptive name, using jpg or png format if possible. Try to limit the size of the file by limiting the resolution to what is necessary for the picture to be clear on screen.
Contributions should be made by creating pull requests on [Github directly](https://github.com/PlanktonPlanet/PlanktoScope/pulls).
## Extensions available
In addition to the common markdown syntax, several extensions are activated. If you want more information on any of them, please follow the linked guides.
- [SmartyPants](https://python-markdown.github.io/extensions/smarty/): Converts ASCII dashes, quotes and ellipses to their HTML entity equivalents.
- [Sane Lists](https://python-markdown.github.io/extensions/sane_lists/): Alters the behavior of the Markdown List syntax to be less surprising.
- [Admonition](https://python-markdown.github.io/extensions/admonition/): Adds rST-style admonitions to Markdown documents.
- [Table of contents](https://python-markdown.github.io/extensions/toc/): Generates a Table of Contents from a Markdown document and adds it into the resulting HTML document.
- [Metadata](https://python-markdown.github.io/extensions/meta_data/): Adds a syntax for defining meta-data about a document.
- [Tables](https://python-markdown.github.io/extensions/tables/): Adds the ability to create tables in Markdown documents.
- [Fenced Code Blocks](https://python-markdown.github.io/extensions/fenced_code_blocks/): Adds a secondary way to define code blocks.

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# Frequently Asked Questions
This FAQ has been compiled to answer common questions about the PlanktoScope project and how you can get involved. We hope you find it useful and we look forward to working with you to advance our knowledge of the oceans!
## I want order a PlantoScope, is there anyone who sells the kits?
The best thing is to say hello in our [Slack Channel](https://planktoscope.slack.com/). Maybe someone is arranging an order or there are currently some available.
## I want to build a PlantoScope, where should I start?
If you have the technical know who then you can build it yourself, the required information can be found here in the documentation. Let others know about your intention to do this and say hello in our [Slack Channel](https://planktoscope.slack.com/), maybe someone is interested and would like to participate.
## Where do i get support or find the necessary tools to build PlantoScope?
To find the necessary tools and knowledge to produce the PlantoScope, consider visiting a [Fablab](https://fablabs.io/labs) or [Hackspaces](https://wiki.hackerspaces.org/List_of_Hacker_Spaces) in your region. These organizations often have a culture of openness and may be willing to support you with your project.
And if you have specific questions or problems, you can always report them in the [Slack Channel](https://planktoscope.slack.com/) and in the best case you will find someone there who can support you.
## I am looking for an older version of the PlantoScope where the housing could still be manufactured with a laser cutter. Where can I find the corresponding design files?
Even though the development is now focused on a more sustainable approach based on recycled wood, the design for the acrylic housing is still available on [Github](https://github.com/PlanktoScope/PlanktoScope/tree/acrylic_case).

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# Plankton Net
A plankton net is a scientific tool used to collect plankton samples from aquatic environments. Plankton are small, drifting organisms that play a vital role in marine ecosystems. They include a diverse range of species, including bacteria, algae, protozoa, and small animals such as crustaceans and mollusks. Plankton nets are designed to capture these tiny organisms as they drift through the water column.
Plankton nets typically consist of a fine mesh net attached to a long, narrow handle. The net is usually cone- or cylinder-shaped, with a small opening at the base and a wider opening at the top. The net is lowered into the water and dragged through the water column, collecting plankton as it goes. The collected plankton is then collected in a sample bottle or container for further study.
Plankton nets can be used in a variety of aquatic environments, including oceans, lakes, and rivers. They are commonly used in scientific research to study the diversity and abundance of plankton in different ecosystems, as well as their role in the food web and the broader ecosystem. Plankton nets are also used in environmental monitoring programs to track changes in plankton populations over time.
![network list](../images/hardware/planktoscope_collecting_device.png)
The simplest device you can use is a plankton net. It should be made of a fine mesh, down to 20 micron. It can be towed behind a boat at low speed (less than 2 knots) or towed by hand in a river or a lake.
Plankton nets can be made easily with a good sewind machine and some hardware.

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# PlanktoScope Hat Hardware
![planktoscope_hero](./images/../../images/hardware/planktoscope_hat_front.png)
## Buses and GPIO pinout
### I2C1 Bus
#### RTC RV-3028-C7
Address 0x52
Configured through a kernel driver.
#### OLED Display
Address 0x3c
#### LED control: LM36011
Address 0x64
Control through specific software, current range from 0 to 376mA in normal mode, up to 1.5A in flash mode.
### SPI0 Bus
#### Motor Controller 0: TMC5160
Chip Enable: SPI0_CE0
Motor Enable: GPIO23
Diagnostic output:
GPIO16 for Error output
GPIO20 for Stall output
#### Motor Controller 1: TMC5160
Chip Enable: SPI0_CE1
Motor Enable: GPIO5
Diagnostic output:
GPIO16 for Error output
GPIO20 for Stall output
### GPIO
#### Fan control
PWM1 control through GPIO13
#### LED Output selection
GPIO18: high for LED1, low for LED2
#### LED Strobe
GPIO22 for pulse
### I2C0 Bus
#### EEPROM M24C32
Address 0x50
For HAT information only.

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# Maintenance and Repair
Instructions for maintaining and repairing an open-source hardware microscope.
## Cleaning the optics
* Begin by turning off the microscope and unplugging it from any power source.
Gently remove any dust or debris using a soft, dry cloth.
* To clean the lenses and other optics, use a lens cleaning solution and a lens cleaning tissue or cloth. Gently wipe the optics in a circular motion, starting from the center and working outward. Avoid applying too much pressure or using a rough cloth, as this can scratch or damage the optics.
* Once you have finished cleaning the optics, use a dry cloth to remove any excess moisture or cleaning solution.
## The Linear Bearings
Linear bearings are mechanical components that allow for smooth, precise linear movement along a shaft or track. Proper inspection and maintenance of linear bearings is essential for ensuring their optimal performance and longevity. In this tutorial, we will discuss how to inspect and maintain linear bearings, including checking for visual and noise issues during operation, cleaning, and lubrication.
### Inspection
Linear bearings should be inspected regularly to ensure that they are functioning properly and are in good condition. There are several key aspects to consider during an inspection:
1. Visual inspection: Look for any visible signs of damage or wear, such as cracks, chips, or deformities in the bearing surfaces or seals.
2. Noise during operation: Listen for any unusual noises or vibrations while the bearing is in use. These may indicate a problem with the bearing or the surrounding machinery.
3. Movement: Check the smoothness and accuracy of the bearing's movement along the shaft or track. Any roughness or deviation from a straight path may indicate a problem with the bearing or the surrounding machinery.
### Maintenance
There are several steps you can take to maintain linear bearings and ensure their optimal performance:
1. Cleaning: Linear bearings should be kept clean to prevent debris from entering and damaging the bearings. Use a clean, dry cloth to wipe away any dirt or debris from the bearing surfaces and seals.
2. Lubrication: Proper lubrication is essential for the smooth operation of linear bearings. Use a high-quality lubricant specifically designed for linear bearings, and follow the manufacturer's recommendations for the frequency and amount of lubrication.
3. Replacement: If a linear bearing is damaged or excessively worn, it should be replaced to ensure the smooth and accurate operation of the machinery.
### Conclusion
Proper inspection and maintenance of linear bearings is essential for ensuring their optimal performance and longevity. By regularly inspecting the bearings for visual and noise issues, and maintaining them through cleaning and lubrication, you can help ensure that your machinery operates smoothly and efficiently.
## The operating system
Tutorial for maintaining and repairing a Debian-based operating system:
1. Connecting to the device:
* To connect to the device, you will need to use a terminal emulator such as PuTTY or GNOME Terminal.
* You will need to know the IP address or hostname of the device, as well as the username and password for an account with admin privileges.
* Once you have entered this information, click "Connect" to establish a connection to the device.
2. System upgrade:
* Once you are connected to the device, enter the command `sudo apt update` to retrieve a list of available software updates.
* Then, enter the command `sudo apt upgrade` to download and install the available updates.
* Wait for the update process to complete, and then restart the system to apply the changes.
3. Analysis of log files with journald:
* Journald is a system service that manages and stores log files on a Debian-based system.
* To view the log files using journald, enter the command `journalctl` in the terminal. This will show the log entries in chronological order.
* You can use the options "--since" and "--until" to specify a time range for the log entries. For example, `journalctl --since yesterday` will show the log entries from the past 24 hours.
* `journalctl -p 3 -xb` will show all log entries that contain the word "error".
4. Available disk space:
* To check the available disk space on the system, enter the command `df -h`. This will show the available space on each disk partition.
* If the available space is low, you can use the command `sudo apt autoremove` to remove unnecessary software packages, or the command `sudo apt clean` to delete temporary files.
5. Service monitoring using systemctl:
* To view the services running on the system, enter the command `systemctl list-units`. This will show a list of all running services.
* To check failed status of all service, use the command `systemctl list-units --failed`.

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# Manufacturing Guide
## PlanktoScope Case
[CNC (computer numerical control) milling machines](https://en.wikipedia.org/wiki/Numerical_control) are used to fabricate parts with precise dimensions and shapes. The configuration of the feed rate and diameter plays a crucial role in the machining process and can significantly affect the quality and efficiency of the production of a workpiece.
![case_parts_00](../images/hardware/planktoscope_case_parts_00.png)
### Manufacturing files
| Files | Description |
| ----------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------- |
| [PlanktoScope-Case.dxf](https://code.curious.bio/curious.bio/planktoscope/raw/branch/din_spec_3105_1/hardware/case/PlanktoScope-Case.dxf) | PlanktoScope Case export for CNC Milling |
### Tools
| Tool | Specification |
| ------------------- | ------------------------------------------------------------ |
| CNC Milling machine | minimum traverse path at a minimum size of 600 mm to 1000 mm |
| End Mill | Ø 6mm |
| End Mill | Ø 3mm |
| End Mill | Ø 2mm |
| End Mill | Ø 1mm |
![case_00](../images/hardware/planktoscope_case_03.jpeg)
### Material
#### Wood
[Valchromat](https://www.investwood.pt/de/valchromat/) is a wood-based composite material made from recycled wood fibers and colored with natural dyes. It is known for its durability, resistance to moisture and decay, and ability to be machined and finished in a similar way to solid wood. Here are some of the key characteristics of valchromat:
- Durability: Valchromat is a highly durable material that is resistant to moisture, decay, and termites, making it ideal for use in outdoor or high-moisture environments.
- Strength: Valchromat has a high mechanical strength, making it suitable for use in structural applications such as flooring, furniture, and doors.
- Machinability: Valchromat can be machined using traditional woodworking tools, such as saws, routers, and drill bits. It can also be finished using sanding, staining, and painting techniques.
- Sustainability: Valchromat is made from recycled wood fibers, which makes it a more sustainable option compared to traditional wood products. It is also produced using an eco-friendly manufacturing process that generates zero emissions.
- Versatility: Valchromat is available in a variety of colors, including shades of red, yellow, green, blue, and black, making it suitable for a wide range of applications and design projects.
![valchromat_colors](../images/hardware/valchromat_colors.jpg)
- When compared to conventional MDF wood, valchromat has a number of advantages. It is more durable and resistant to moisture and decay, making it a better choice for use in outdoor or high-moisture environments. Valchromat is also more sustainable, as it is made from recycled wood fibers.
- Valchromat can be processed using a CNC router in a similar way to MDF wood. However, it is important to consider the specific characteristics of valchromat when setting up the CNC router, such as the appropriate cutting speed and feed rate.
For the specific use case of the PlanktoScope Case, valchromat was used with a **thickness of 8mm**. This thickness may be suitable for a variety of applications, depending on the specific requirements and design of the project.
In summary, valchromat is a durable, strong, and versatile wood-based composite material that can be machined and finished in a similar way to solid wood. It is available in a variety of colors and is a more sustainable alternative to traditional wood products. When processed using a CNC router, it is important to consider the specific characteristics of valchromat in order to achieve the desired results.
#### Finishing
[Rubio Monocoat Plus](https://www.rubiomonocoat.com/) is a wood finishing product that is designed to provide a durable, natural-looking finish to wood surfaces. It is made from plant-based oils and pigments, which give it a unique, transparent finish that enhances the natural beauty of the wood.
One of the key features of Rubio Monocoat Plus is its versatility and ease of use. It can be applied to a wide range of wood species, including hardwoods and softwoods, and can be used on both indoor and outdoor surfaces. It is also easy to apply, with a simple one-coat application process that allows users to achieve a professional-grade finish in a matter of hours.
Rubio Monocoat Plus is also environmentally friendly, with a low VOC (volatile organic compound) content and a biodegradable formula. This makes it a popular choice for those who are looking for a sustainable and eco-friendly wood finishing solution.
We use Rubio Monocoat Plus as a finishing product for Valchromat.
### CNC workflow
Here is a step-by-step guide on how to configure the feed rate and the diameter of the end mill of a CNC milling machine for the production of a workpiece, using the specified tools and configuration:
1. Select the appropriate end mill: The end mill should be selected based on the material and shape of the workpiece, as well as the desired level of precision. For this specific production, the following end mills will be used:
- 6mm end mill for straight flats
- 2mm end mill for inner contours
- 1mm end mill for small holes
2. Determine the feed rate: The feed rate is the speed at which the end mill moves along the surface of the workpiece and is usually measured in millimeters per minute (mm/m). The appropriate feed rate will depend on the diameter of the end mill and the material and thickness of the workpiece. For this specific production, the following feed rates will be used:
- 1500mm/min for 1-2mm end mills
- 2500mm/min for 3mm end mills
- 3500mm/min for 6mm end mills
3. Load the end mill: Once the appropriate end mill has been selected, it can be loaded onto the spindle of the CNC milling machine.
4. Set the workpiece: The workpiece should be securely clamped onto the table of the CNC milling machine.
5. Set the machine parameters: The feed rate and end mill diameter should be entered into the machine's control panel or included in the machining program.
6. Begin machining: The machining process should be carried out in the following sequence:
- Mill the screw holes with a 2mm end mill and then with a 3mm end mill
- Mill the corners with a 2mm end mill
- Mill everything else with a 3mm end mill
By following these steps, you can properly configure the feed rate and the diameter of the end mill of a CNC milling machine for the production of a workpiece. It is important to follow the manufacturer's recommendations and guidelines for the specific CNC milling machine being used, as well as to use proper safety measures while operating the machine.
![planktoscope_case_00.png](../images/hardware/planktoscope_case_00.png)
### Finnish of the case parts
#### Requirements for case parts
##### Case tools
- Hammer
- Air Compressor
- Rubber gloves
- Paper carpet pad
- Clean piece of cotton fabric
- Support material for drying the parts
##### Case part parts
- all case parts
- Rubio Monocoat Oil Plus 2C
- Rubio Monocoat Accelerator Component B
- Magnets
- Square nuts
#### Clean
![](../images/manufacturing_guide/IMG_20230205_114522_026.jpg)
#### Stir
![](../images/manufacturing_guide/IMG_20230205_121506_912.jpg)
![](../images/manufacturing_guide/IMG_20230205_121600_985.jpg)
#### Apply
![](../images/manufacturing_guide/IMG_20230205_121740_849.jpg)
![](../images/manufacturing_guide/IMG_20230205_122339_866.jpg)
![](../images/manufacturing_guide/IMG_20230205_123231_263.jpg)
#### Dry
![](../images/manufacturing_guide/IMG_20230205_141852_172.jpg)
#### Inserting the screws
![](../images/manufacturing_guide/IMG_20230206_182410_394.jpg)
![](../images/manufacturing_guide/IMG_20230206_194436_007.jpg)
![](../images/manufacturing_guide/IMG_20230206_195227_606.jpg)
#### Inserting the magnets
![](../images/manufacturing_guide/IMG_20230206_185209_322.jpg)
![](../images/manufacturing_guide/IMG_20230206_185827_022.jpg)
![](../images/manufacturing_guide/IMG_20230206_190002_449.jpg)
![](../images/manufacturing_guide/IMG_20230206_191831_326.jpg)
![](../images/manufacturing_guide/IMG_20230206_191905_086.jpg)
![](../images/manufacturing_guide/IMG_20230206_191911_092.jpg)
![](../images/manufacturing_guide/IMG_20230206_192122_827.jpg)
![](../images/manufacturing_guide/IMG_20230206_191942_446.jpg)
![](../images/manufacturing_guide/IMG_20230206_192115_770.jpg)
![](../images/manufacturing_guide/IMG_20230206_192048_827.jpg)
![](../images/manufacturing_guide/IMG_20230206_190821_839.jpg)
![](../images/manufacturing_guide/IMG_20230206_191601_928.jpg)
![](../images/manufacturing_guide/IMG_20230206_192512_587.jpg)
![](../images/manufacturing_guide/IMG_20230206_192610_421.jpg)
#### Package Housing part
![](../images/manufacturing_guide/IMG_20230206_212202_209.jpg)
![](../images/manufacturing_guide/IMG_20230206_211854_910.jpg)
## PlanktoScope Hat
Welcome to the PCB production manual for the PlanktoScope Hat!
![planktoscope_hat_front.png](../images/hardware/planktoscope_hat_front.png)
![planktoscope_hat_back.png](../images/hardware/planktoscope_hat_back.png)
A [PCB (printed circuit board)](https://en.wikipedia.org/wiki/Printed_circuit_board) is a crucial component of many electronic devices, providing a platform for connecting and mounting electronic components. The PCB production process involves several steps, including designing the PCB layout, fabricating the PCB, and assembling the electronic components onto the PCB.
The raw materials used in PCB production include copper sheets, fiberglass sheets, and various chemicals for etching and plating. These materials are used to create the circuitry patterns on the PCB.
There are two main types of electronic components that can be mounted onto a PCB: [thru-hole components](https://en.wikipedia.org/wiki/Through-hole_technology) and [surface mount components](https://en.wikipedia.org/wiki/Surface-mount_technology). Thru-hole components have leads that are inserted through holes in the PCB and soldered to the other side, while surface mount components are soldered directly onto the surface of the PCB. The choice between thru-hole and surface mount components depends on the specific requirements of the device being produced.
!!! note
Please note that this document describes a two-part production of the PCB. To reduce costs, the through hole components are assembled manually as described here. Depending on your budget and the services offered by the manufacturing company, this can also be ordered in the production of the PCB.
### Manufacturing files
| Files | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------- |
| [Planktoscope-Hat-bom.csv](https://code.curious.bio/curious.bio/planktoscope/raw/branch/din_spec_3105_1/hardware/hat/Planktoscope-Hat-bom.csv) | The list of used SMD components |
| [Planktoscope-Hat gerber files](https://code.curious.bio/curious.bio/planktoscope/src/branch/din_spec_3105_1/hardware/hat/assembly) | The exported CAD and CAM data of the PCB design |
| [Planktoscope-Hat assembly files](https://code.curious.bio/curious.bio/planktoscope/src/branch/din_spec_3105_1/hardware/hat/assembly) | The SMD assembly instructions |
### PCB manufacturing process
#### Placing an order
To order a PCB board including assembly, follow these steps:
- Select a manufacturing company based on your local availability, budget, delivery dates, and services such as assembly.
!!! note
If you need assistance with selecting a company, contact us. We can provide you with a list of companies we have worked with in the past.
- Create a customer account if you do not already have one. Ensure to specify the correct tax, contact, and delivery information.
!!! warning
It is especially crucial to provide correct contact information, including a phone number if possible. Most manufacturing companies provide excellent customer service and will be happy to assist you during the order process.
- Create a project and select the quantity of PCB boards you need for production.
- Configure the order based on the values specified in this document.
- Upload the bill of material (BOM) and validate the component availability.
!!! warning
It is crucial that you use the exact IC's like the RTC and EEPROM we specified. If a component is "end of life" (EOL), do not hesitate to contact us so we can help you find an alternative solution. For all other components, you are welcome to choose alternatives providet by the manufacturing company.
!!! info
The component costs will now be calculated, and the price should be displayed.
- Upload the gerber files provided as a zip file in the repository under the following link.
- Upload the assembly instructions provided as a zip file in the repository under the following link.
- Check that there are no missing references in your order configuration.
- Place the order based on your delivery requirements.
- Select a payment method and complete the order process.
#### Configuration
The following configuration parameters can be used for the production of the PCB.
!!! info
Please note that the naming may vary depanding on the manufacturing company you used and are only intended to provide you with support. You can, of course, adjust the parameters as you see fit.
##### Board dimensions
65 mm x 100 mm
##### Circuit specifications
| Property | Value |
| -------------------------------------- | ---------- |
| Material | FR4 |
| Thickness | 1.6 mm |
| Finish | Chem. gold |
| Number of layers | 2 |
| Specific stackup | sans |
| SMD sides | top |
| Finished external copper thickness (µ) | 35 µm |
| Internal copper thickness (µ) | without |
| IPC Class | Class 2 |
##### Solder mask
| Property | Value |
| ------------- | --------- |
| Solder mask | TOP + BOT |
| Mask colour | green |
| Peelable mask | without |
##### Marking
| Property | Value |
| ---------------- | --------- |
| Silkscreen (ink) | TOP + BOT |
| Ink colour | white |
| ROHS marking | without |
| UL marking | without |
| Date marking | without |
##### Specific options
| Property | Value |
| -------------------------- | --------- |
| Space between tracks | > 0.15 mm |
| Min. drill hole size | > 0.20 mm |
| Blind via | with out |
| Cross blind | no |
| Burried via | na |
| Impedance control | no |
| Edge plating | no |
| Press-fit | no |
| Carbon | without |
| Via Fill | without |
| Beveled edge | without |
| Contersunk holes | without |
| Contersunk holes (qty/PCB) | without |
| Metallographic section | without |
| Gold fingers (thickness) | without |
| Gold fingers (qty/PCB) | without |
#### Quality assurance
To ensure the quality of the produced PCB, request data validation from the customer support team. They can provide you with image files like the following to visually verify the manufacturing files you provide.
!!! warning
This step must be requested directly after completing the order process and confirmed promptly. Otherwise, the delivery date will be postponed or the order may be put on hold completely.
##### Top
![Planktoscope-Hat-validation-top.png](../images/hardware/Planktoscope-Hat-validation-top.png)
##### Bottom
![Planktoscope-Hat-validation-bottom.png](../images/hardware/Planktoscope-Hat-validation-bottom.png)
##### Copper layer 1
![Planktoscope-Hat-validation-layer1.png](../images/hardware/Planktoscope-Hat-validation-layer1.png)
##### Copper layer 2
![Planktoscope-Hat-validation-layer2.png](../images/hardware/Planktoscope-Hat-validation-layer2.png)
##### Mechanical
![Planktoscope-Hat-validation-mechanical.png](../images/hardware/Planktoscope-Hat-validation-mechanical.png)
##### Component placement
![Planktoscope-Hat-validation-component-placement.png](../images/hardware/Planktoscope-Hat-validation-component-placement.png)
### Assembly of the Thru-Hole components
#### Thru-Hole Requirements
![](../images/manufacturing_guide/IMG_20230210_130428_325.jpg)
##### Thru-Hole tools
- [professional Soldering iron](https://en.wikipedia.org/wiki/Soldering_station)
- [solder](https://en.wikipedia.org/wiki/Solder) with flux
- [Helping hand](<https://en.wikipedia.org/wiki/Helping_hand_(tool)>) or [Breadboard](https://en.wikipedia.org/wiki/Breadboard)
##### Thru-Hole parts
| Files | Description |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------- |
| [Planktoscope-Hat-throughhole.csv](https://code.curious.bio/curious.bio/planktoscope/raw/branch/din_spec_3105_1/hardware/hat/Planktoscope-Hat-throughhole.csv) | The list of used SMD components |
!!! warning
When you solder this for the first time, take special care not to damage the board.
!!! info
To learn how to solder we recommend you the awesome [Comic "Soldering is easy" by Mitch Altmal, Andie Nordgren and Jeff Keyzer](https://mightyohm.com/soldercomic/)
#### Soldering of the stepper motor driver
![](../images/manufacturing_guide/IMG_20230210_131022_517.jpg)
Unpack the motor driver and the connector strips and take the breadboard aside.
---
![](../images/manufacturing_guide/IMG_20230210_131109_910.jpg)
Plug the connectors with the appropriate distance to the breadboard.
!!! Info
The breadboard supports you during soldering to ensure the spacing and angle of the connectors, alternatively you can also use a third hand.
---
![](../images/manufacturing_guide/IMG_20230210_133453_815.jpg)
Now position the motor driver on the connector strips of the beadboard.
!!! Warning
Make sure that the larger chip labeled trimatik is positioned on the bottom of the board and the four smaller chips are positioned on the top of the board as shown in the picture.
---
![](../images/manufacturing_guide/IMG_20230210_133632_016.jpg)
Now solder all pins of the connector strip.
!!! Info
Soldering is sometimes like eating with chopsticks 🥢. It takes a bit of practice, but with time you learn how to hold the workpiece in place with one free finger and apply the solder with another, and then use the other hand to move the soldering iron to the workpiece and solder it.
!!! Tip
You can also solder one pin on one side and then the opposite one to fix your workpiece, this ensures that nothing accidentally moves.
---
#### Soldering of the motor driver sockets
![](../images/manufacturing_guide/IMG_20230210_134008_727.jpg)
Now take the PlanktoScope Hat board and the female connector of the stepper motor driver and position them as shown in the picture.
---
![](../images/manufacturing_guide/IMG_20230210_134140_898.jpg)
Now put the previously soldered motor driver on the socket connector to fix it for the soldering process. Turn the board as shown in the picture and place it carefully.
---
![](../images/manufacturing_guide/IMG_20230210_134243_277.jpg)
Now solder all pins of the connector strip.
!!! Info
Soldering is sometimes like eating with chopsticks 🥢. It takes a bit of practice, but with time you learn how to hold the workpiece in place with one free finger and apply the solder with another, and then use the other hand to move the soldering iron to the workpiece and solder it.
!!! Tip
You can also solder one pin on one side and then the opposite one to fix your workpiece, this ensures that nothing accidentally moves.
---
![](../images/manufacturing_guide/IMG_20230210_135810_493.jpg)
Repeat the procedure with the second motor driver. The end result should look like this.
---
#### Soldering the connection sockets
![](../images/manufacturing_guide/IMG_20230210_135925_885.jpg)
Now solder the motor driver sockets, inserting the connector into the holes as shown.
---
![](../images/manufacturing_guide/IMG_20230210_140051_746.jpg)
Turn the board over and hold the loose connector while soldering it. Repeat the procedure with the second motor connector.
!!! Info
Soldering is sometimes like eating with chopsticks 🥢. It takes a bit of practice, but with time you learn how to hold the workpiece in place with one free finger and apply the solder with another, and then use the other hand to move the soldering iron to the workpiece and solder it.
---
![](../images/manufacturing_guide/IMG_20230210_140238_720.jpg)
Repeat the procedure with the power connector. The end result should look like this.
---
![](../images/manufacturing_guide/IMG_20230210_140454_602.jpg)
Repeat the procedure with the led connector. The end result should look like this.
---
#### Soldering the Raspberry Pi connector
![](../images/manufacturing_guide/IMG_20230210_141753_889.jpg)
Now solder the Raspberry Pi header connector with all 20 pins.
!!! Warning
Be extremely careful when soldering the connections, make sure you don't accidentally bridge several contacts because you used too much solder or have cold solder joints because you had too little solder or too little heat.
---
#### Install and solder the cooling fan
<!-- ![](../images/manufacturing_guide/xxxxxxxxxxxxxxxx.jpg) -->
Install the fan with the four screws and nuts.
!!! Warning
Pay attention to the running direction with the arrow marking on the side of the fan. The fan should blow on the cooler of the Raspberry Pi.
---
<!-- ![](../images/manufacturing_guide/xxxxxxxxxxxxxxxx.jpg) -->
Cut off the excess cable of the fan and leave about 6 cm.
---
![](../images/manufacturing_guide/IMG_20230210_144404_281.jpg)
Feed the fan cable through the hole provided, check if you can reach the contacts on the board without any problems and trim it further if necessary and enisolate the ends.
---
![](../images/manufacturing_guide/IMG_20230210_144605_565.jpg)
Solder the fan cables according to the marking and color codes ⚫ GND, 🔴 VCC, 🟡 RPM, 🔵 PWM.
!!! note
If your fan doesn't have a 🔵 PWM connector, then that's not a problem, you can just leave it out.
---
#### Solder the display connector
![](../images/manufacturing_guide/IMG_20230210_144803_799.jpg)
Insert the pin headers into the holes provided, hold them in place, carefully turn the board over and solder the connector.
!!! note
If you do not use an OLED display, you do not need to solder the connector.
---
#### Solder the configuration option jumpers
<!-- ![](../images/manufacturing_guide/XXXXXXXXXXXXXXXXXXX.jpg) -->
Insert the pin headers into the holes provided, hold them in place, carefully turn the board over and solder the connector.
!!! note
If you do not use an OLED display, you do not need to solder the connector.
---
#### You have finished soldering the components
![](../images/manufacturing_guide/IMG_20230210_144924_538.jpg)
The assembly of the thru-hole components for the planktoscope hat is now complete. The end result should look like this.
---
## PlanktoScope Hard case
### Hard case Requirements
#### Hard case tools
- double sided adhesive tape
#### Hard case parts
- Hard case
![Case and double sided adhesive tape](../images/manufacturing_guide/IMG_20230129_163747_902.jpg)
### Foam preparation
![Divide foam](../images/manufacturing_guide/IMG_20230129_163501_186.jpg)
Cut the foam block at the outer edge by gently tearing it apart with your fingers.
!!! Warning
Be careful the foam tears easily and can not be repaired.
!!! Tip
You can try in the middle of the foam block to see how the material can be cut through before you peel off with the edge.
---
![Foam glue](../images/manufacturing_guide/IMG_20230129_163337_964.jpg)
Now lay a layer of two-sided adhesive tape on the upper inside edge of the case, with which we can later attach the show fabric.
---
![Insert foam](../images/manufacturing_guide/IMG_20230129_163710_699.jpg)
Now insert the foam edge in to the case and glue it to the outer wall.
!!! Note
Before you fix the foam, position it completely and check that it is placed flush with the edge of the case.
---
## Kit composition
<!-- ![all kit parts](../images/manufacturing_guide/XXXXX.jpg) -->
Now divide all the components for a kit and pack it in the hard case.
---

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