planktoscope/README.md

# An open and affordable imaging platform for citizen oceanography

![PlanktoScope Render](docs/readme/planktoscope_cad.webp)

![Plankton collage](docs/readme/plankton_collage.webp)


# What is this?
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.

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.


## Get the papers!
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).

|[![PlanktoScope Preprint](docs/readme/planktoscope_pub.webp)](https://www.biorxiv.org/content/10.1101/2020.04.23.056978v1)|[![PlanktonPlanet Preprint](docs/readme/planktonplanet_pub.webp)](https://www.biorxiv.org/content/10.1101/2020.08.31.263442v1)|
|--------|--------|


# Key Features
- Image small animals and algae living in water
- Focus stage control
- Pump control
- Automatic image capture
- Automatic segmentation

# How do I build one?
You can access the complete documentation on [Read The Docs](https://planktonscope.readthedocs.io/).

# How do I get involved?
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/PlanktonScope/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.
First README rewrite 2020-09-28 14:53:59 +02:00			`# An open and affordable imaging platform for citizen oceanography`
README.md: improve documentation on setup, part 1 2020-05-29 23:05:41 +02:00
readme: transition to webp for lighter pictures 2020-10-06 16:55:58 +02:00			`![PlanktoScope Render](docs/readme/planktoscope_cad.webp)`
README.md: improve documentation on setup, part 1 2020-05-29 23:05:41 +02:00
readme: transition to webp for lighter pictures 2020-10-06 16:55:58 +02:00			`![Plankton collage](docs/readme/plankton_collage.webp)`
README.md: improve documentation on setup, part 1 2020-05-29 23:05:41 +02:00

First README rewrite 2020-09-28 14:53:59 +02:00			`# What is this?`
			`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.`

			`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.`

Various small updates 2020-09-28 21:35:19 +02:00
			`## Get the papers!`
First README rewrite 2020-09-28 14:53:59 +02:00			`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).`

readme: transition to webp for lighter pictures 2020-10-06 16:55:58 +02:00			`\|[![PlanktoScope Preprint](docs/readme/planktoscope_pub.webp)](https://www.biorxiv.org/content/10.1101/2020.04.23.056978v1)\|[![PlanktonPlanet Preprint](docs/readme/planktonplanet_pub.webp)](https://www.biorxiv.org/content/10.1101/2020.08.31.263442v1)\|`
First README rewrite 2020-09-28 14:53:59 +02:00			`\|--------\|--------\|`


			`# Key Features`
Features 2020-10-07 12:43:59 +02:00			`- Image small animals and algae living in water`
			`- Focus stage control`
			`- Pump control`
			`- Automatic image capture`
			`- Automatic segmentation`
First README rewrite 2020-09-28 14:53:59 +02:00
			`# How do I build one?`
			`You can access the complete documentation on [Read The Docs](https://planktonscope.readthedocs.io/).`
how to get involved 2020-09-28 22:03:41 +02:00
			`# How do I get involved?`
			`There are several ways to join the development effort, share your progress with your build or just ask for help.`

Update Google Form link to join the slack 2021-02-19 17:29:36 +01:00			`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).`
how to get involved 2020-09-28 22:03:41 +02:00
Update Google Form link to join the slack 2021-02-19 17:29:36 +01:00			`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/PlanktonScope/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.`