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# PlanktoScope: Open and Affordable Quantitative Imaging Platform
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SPDX-License-Identifier: CC-BY-SA-4.0
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# An open and affordable imaging platform for citizen oceanography
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## What are Plankton?
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| CI/CD | [](https://github.com/PlanktoScope/PlanktoScope/actions/workflows/test.yml) [](https://github.com/PlanktoScope/PlanktoScope/actions/workflows/build.yml) |
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| Package | [](https://pypi.org/project/planktoscope/) [](https://pypi.org/project/planktoscope/) |
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| Meta | [](https://github.com/pypa/hatch) [](https://github.com/psf/black) [](https://github.com/ambv/black) [](https://github.com/pycqa/isort) [](<https://spdx.org/licenses/>) |
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_"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**
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## What is this?
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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.
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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 $500 in parts.
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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.
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## What is a PlanktoScope?
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## Get the papers
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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.
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The PlanktoScope has been described in a paper available on the [bioRxiv preprint server](https://www.biorxiv.org/content/10.1101/2020.04.23.056978v1). The first results of this program and its outline are also available as a [preprint](https://www.biorxiv.org/content/10.1101/2020.08.31.263442v1).
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[Learn more about how it works](https://www.planktoscope.org/how-it-works)
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| [](https://www.biorxiv.org/content/10.1101/2020.04.23.056978v1) | [](https://www.biorxiv.org/content/10.1101/2020.08.31.263442v1) |
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## Read the Paper
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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.
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DOI: [https://doi.org/10.3389/fmars.2022.949428](https://doi.org/10.3389/fmars.2022.949428)
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## Key Features
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## Key Features
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- Image small animals and algae living in water
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Here are some key features of the PlanktoScope:
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- Focus stage control
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- Pump control
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- Automatic image capture
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- Automatic segmentation
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## How do I build one?
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1. **Low cost**: The PlanktoScope is designed to be affordable, with parts costing under $1000.
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2. **Modular**: The PlanktoScope is modular, meaning it can be easily reconfigured to meet the changing needs of users.
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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.
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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.
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5. **High-throughput**: The PlanktoScope is capable of high-throughput quantitative imaging, allowing users to analyze large numbers of samples quickly and efficiently.
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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.
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7. **Portable**: The PlanktoScope is small and portable, making it easy to transport and use in the field.
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8. **Ease of use**: The PlanktoScope is designed to be easy to use, with instructions for assembly and use available on the PlanktoScope website.
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## How do I get one?
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You can access the complete documentation on [Read The Docs](https://planktonscope.readthedocs.io/).
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You can access the complete documentation on [Read The Docs](https://planktonscope.readthedocs.io/).
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|Get the kit|Assemble your kit|Start your machine|
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## How do I get involved?
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## Getting Involved
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There are several ways to join the development effort, share your progress with your build or just ask for help.
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There are several ways you can join the development effort and contribute to this project.
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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).
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### Communication Platform
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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.
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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).
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## License: Our work is fully open source
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### Reporting Issues
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Depending on the material they cover, different licenses apply to the files of this repository.
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If you have identified a bug in the software or hardware, please open an issue in this repository to report it.
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If you make any change for your use, please fork this repository and publish your improvements. It will help others, and we can integrate those changes in this repository if needed.
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### Contributing to Development
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Also, all licenses are contaminating, if you want to use any of this material for a project that you cannot open-source, please contact us using Slack so we can see what can be done to help you and your project.
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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.
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## Hardware files
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## License Information
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All hardware files and documentation (everything in the `hardware` directory) is released under a [CERN-OHL-S-2.0 license](https://ohwr.org/cern_ohl_s_v2.txt).
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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.
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## Software source
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### Hardware Files
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The source code (everything in the directories `flows` and `scripts`) is released under a [GPL-3.0 license](https://www.gnu.org/licenses/gpl-3.0.en.html).
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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.
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## Everything else (documentation, pictures, etc...)
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### Software Source Code
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Everything else is released under a [Creative Commons CC-BY-SA license](https://creativecommons.org/licenses/by-sa/4.0/).
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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.
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### Other Materials
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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.
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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.
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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.
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# Open and frugal modular imaging platform for citizen oceanography
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# PlanktoScope: Open and Affordable Quantitative Imaging Platform
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