latest changes

docs/community/community.md

@@ -1,34 +0,0 @@
-# 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 $500, 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.
-
-<table>
-    <tr>
-        <td>
-
-## Engage on GitHub
-
-<a href="https://github.com/PlanktoScope/PlanktoScope" rel="GitHub">![GitHub](../images/community/github.png)</a>
-
-Feel free to visit the **GitHub** and engage if you want.
-        </td>
-        <td>
-
-## Chat on Slack
-
-<a href="https://planktoscope.slack.com" rel="Slack">![Slack](../images/community/slack.png)</a>
-
-The community is using **Slack** to communicate.
-        </td>
-        <td>
-
-## Classify on EcoTaxa
-
-<a href="https://ecotaxa.obs-vlfr.fr/register" rel="EcoTaxa">![EcoTaxa](../images/community/ecotaxa.png)</a>
-
-To join **EcoTaxa**, you just need to create an account.
-        </td>
-    </tr>
-</table>

docs/contribute/hardware_development.md

@@ -1,6 +1,6 @@
 # Hardware Development
 
-![planktoscope_hero](../images/project_description/planktoscope_versions.png)
+![planktoscope_hero](../images/project_description/planktoscope_versions_01.png)
 
 ## PlanktoScope Case
 

docs/contribute/software_architecture.md

@@ -1,26 +0,0 @@
-<!--
-SPDX-License-Identifier: CC-BY-SA-4.0
--->
-
-# Our software architecture
-
-## Node-Red
-
-![](../images/logos/node-red.svg){ width="100" }
-
-[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.
-
-## 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.

docs/contribute/software_development.md

@@ -11,3 +11,24 @@ If you want to join us, have a look at the [currently opened issues](https://git
 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
+
+![](../images/logos/node-red.svg){ width="100" }
+
+[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.
+
+## 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.

docs/hardware/hat_hardware.md

@@ -4,6 +4,9 @@ SPDX-License-Identifier: CC-BY-SA-4.0
 
 # PlanktoScope Hat Hardware
 
+![planktoscope_hero](./images/../../images/hardware/planktoscope_hat_front.png)
+![planktoscope_hero](./images/../../images/hardware/planktoscope_hat_back.png)
+
 ## Buses and GPIO pinout
 
 ### I2C1 Bus

docs/index.md

@@ -1,11 +1,55 @@
 ![planktoscope_hero](images/project_description/planktoscope_hero.png)
 
-An open and affordable imaging platform for citizen oceanography
+# Open and frugal modular imaging platform for citizen oceanography
 
-# What is this?
+## 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
+
+Helping fix 30-50% of the worlds carbon dioxide and providing the foundation of a global food chain, plankton comprise the largest daily movement of biomass in the world as they traverse the oceans. The shapes, colors, and movements of these billions of creatures are as vast as the seas that sustains them. Understanding plankton is crucial to understanding the world around us, and the effect we have on that world. A hurdle for this type of study has been the sheer scale of area to explore, and the limited resources of research fleets and specialized equipment. By developing a way to scale up high quality visual exploration and documentation we can greatly increase our understanding of the complicated web of life around us, and how we are in turn impacting it.
+
+## What is a PlanktoScope?
 
 The PlanktoScope is an open-source, affordable imaging platform for citizen oceanography. It's built around a Raspberry Pi, a couple of HATs, some stepper motors and a few centimeters of silicon tubes. Its cost is at about $800 in parts.
 
 The goal of the PlanktoScope is to allow citizen to engage in scientific programs, either at sea or onshore. You can use the PlanktoScope to image the different species of Plankton living in a body of water.
 
-![planktoscope_hero](images/project_description/planktoscope_hero.png)
+![planktoscope_hero](images/project_description/planktoscope_architecture.png)
+
+## The build and use documentation
+
+You can find here more information about how to build your own PlanktoScope.
+
+### Setup
+
+- [How to setup your PlanktoScope the easy way](./software/easy_install.md)
+- [How to setup your PlanktoScope the hard way (also known as the Expert's path)](./software/expert_setup.md)
+- [Some information about how to setup a remote access](./usage/remote_access.md)
+
+### Build your machine
+
+- [Assembly Guide](./hardware/assembly_guide.md)
+
+### Usage
+
+- [Information about collection devices](./hardware/collection_devices.md)
+
+### Under the hood
+
+- [Software Development](./contribute/software_development.md)
+- [MQTT Messages](./usage/mqtt_messages.md)
+- [Create Master SD Card or backup your PlanktoScope](./software/create_sd.md)
+- How does the segmentation works (soon)
+
+## Changelog
+
+- [Changelog](./changelog.md)
+
+## Contribute
+
+- [Find out how to contribute to this documentation and help edit it](./contribute/writing_documentation.md)
+- [Contribute to the code, here is the getting started](./contribute/software_development.md)
+
+## License
+
+- [More information about the licenses that we use](./license.md)

docs/introduction/device_specification.md

@@ -8,11 +8,11 @@
 
 ## Hardware
 
-* 4 Core ARM-Cortex-A72 Processor with 1,50 GHz
+* [4 Core ARM-Cortex-A72 Processor](https://www.raspberrypi.com/products/raspberry-pi-4-model-b/) with 1,50 GHz
 * 4 GB Arbeitsspeicher (depending on the purchased version)
 * 64 GB Flash memory (depending on the purchased version)
 * [Sony IMX477R](https://www.raspberrypi.com/products/raspberry-pi-high-quality-camera/) Image sensor with 12.3MP
-* M12-Mount Optiken mit 16 und 25 mm Linsen
+* M12 mount optics with 16 and 25 mm lenses
 * Automatic focus via linear guide
 * automatic sampling via peristaltic pump
 * the case is made of wood fiberboard
@@ -35,9 +35,9 @@
 
 ## License
 
-* Hardware: CERN Open Hardware Licence
+* Hardware: [CERN Open Hardware Licence](https://cern-ohl.web.cern.ch/home)
-* Software: GNU General Public License
+* Software: [GNU General Public License](https://www.gnu.org/licenses/gpl-3.0.html)
-* Dokumentation: Creative Commons Attribution-ShareAlike
+* Dokumentation: [Creative Commons Attribution-ShareAlike](https://creativecommons.org/licenses/by-sa/4.0/)
 
 ## Certification
 
@@ -50,9 +50,9 @@
 
 ## System Requirements
 
-* a Web-Browser to control the device (like a Notebook, Smartphone or tablet)
+* a Web-Browser to control the device (like a Notebook, Smartphone or Tablet)
 
 ## Accessories
 
-* [Collector device]()
+* [Collector device](../hardware/collection_devices.md)
 * [12v Power Bank]()

docs/introduction/research.md

@@ -1,13 +1,31 @@
 # Research
 
-## Plankton Planet: ‘seatizen’ oceanography to assess open ocean life at the planetary scale
-
-* assets/2020.08.31.263442v1.full.pdf
-
-## PlanktoScope: Affordable Modular Quantitative Imaging Platform for Citizen Oceanography
-
-* assets/fmars-09-949428.pdf
-
 ## PlanktonScope: Affordable modular imaging platform for citizen oceanography
 
-* assets/2020.04.23.056978v1.full.pdf
+|            |                                                                                                                 |
+| ---------- | --------------------------------------------------------------------------------------------------------------- |
+| **Author** | Thibaut Pollina, Adam G. Larson, Fabien Lombard, Hongquan Li, Sebastien Colin, Colomban de Vargas, Manu Prakash |
+| **Date**   | 23 April 2020                                                                                                   |
+| **DOI**    | <https://doi.org/10.1101/2020.04.23.056978>                                                                     |
+
+<a href="/assets/2020.04.23.056978v1.full.pdf" rel="2020.04.23.056978v1.full.pdf">![2020.04.23.056978v1.full.pdf](../images/research/2020.04.23.056978v1.full.png)</a>
+
+## Plankton Planet: ‘seatizen’ oceanography to assess open ocean life at the planetary scale
+
+|            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
+| ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Author** | Colomban de Vargas, Thibaut Pollina, Sarah Romac, Noan Le Bescot, Nicolas Henry, Calixte Berger, Sébastien Colin, Nils Haëntjens, Margaux Carmichael, David Le Guen, Johan Decelle, Frédéric Mahé, Emmanuel Malpot, Carole Beaumont, Michel Hardy, the planktonauts, the Plankton Planet team, Damien Guiffant,Ian Probert, David F. Gruber, Andy Allen, Gabriel, Gorsky, Mick Follows, Barry B. Cael, Xavier Pochon, Romain Troublé, Fabien Lombard, Emmanuel Boss, Manu Prakash |
+| **Date**   | 01 September 2020                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| **DOI**    | <https://doi.org/10.1101/2020.08.31.263442>                                                                                                                                                                                                                                                                                                                                                                                                                                       |
+
+<a href="/assets/2020.08.31.263442v1.full.pdf" rel="2020.08.31.263442v1.full.pdf">![2020.08.31.263442v1.full.pdf](../images/research/2020.08.31.263442v1.full.png)</a>
+
+## PlanktoScope: Affordable Modular Quantitative Imaging Platform for Citizen Oceanography
+
+|            |                                                                                                                              |
+| ---------- | ---------------------------------------------------------------------------------------------------------------------------- |
+| **Author** | Thibaut Pollina, Adam G. Larson, Fabien Lombard, Hongquan Li,David Le Guen, Sébastien Colin, Colomban de Vargas,Manu Prakash |
+| **Date**   | 22 July 2022                                                                                                                 |
+| **DOI**    | <https://doi.org/10.3389/fmars.2022.949428>                                                                                  |
+
+<a href="/assets/fmars-09-949428.pdf" rel="fmars-09-949428.pdf">![fmars-09-949428.pdf](../images/research/fmars-09-949428.png)</a>

docs/usage/getting_started.md

@@ -4,7 +4,7 @@ SPDX-License-Identifier: CC-BY-SA-4.0
 
 # Getting started with using the machine
 
-Congratulations! You have finished assembling your machine, now is the time to test it and learn how to use it!
+Congratulations! You have [finished assembling](../hardware/assembly_guide.md) your machine, now is the time to test it and learn how to use it!
 
 ## How to connect to and control the machine
 

docs/usage/ui_guide.md

@@ -4,7 +4,7 @@ SPDX-License-Identifier: CC-BY-SA-4.0
 
 # User interface guide
 
-Starting with the release of v2.2, a new user interface brings a whole new user interface. This guide will help you get familiar with it.
+Starting with the [release of v2.2](https://github.com/PlanktoScope/PlanktoScope/releases/tag/v2.2), a new user interface brings a whole new user interface. This guide will help you get familiar with it.
 
 ![Home](../images/ui_guide/home.webp)