Tested and tried Open Source tools for academic research

HI folks!

There are starting conversations here at Sussex on how to bring more open science/open source tools to the “main stage” at the School of Life Sciences.

One of the proposed initiatives is to compile a list of mature Open Source projects, so that researchers could have a fast and easy overview of what is available for their research projects. The idea is that by increasing this flow of information we can increase adoption and over time the opinion people have on open source projects.

I have a rough idea of these types of projects for neuroscience (see below), but was wondering if people who are in other fields, could/would like to collaborate with suggestions of tools they have already used/tested and know are ready for use by a “general” audience that is not tech savvy (as in researchers that do not want to code/compile nor tinker - crazy, I know).

This post is a wiki! Feel free to add more resources, comments and suggestions!


Project contact point use case field
Pyphotometry photometry experiments neuroscience
OpenEphys electrophysiology experiments neuroscience
OpenTrons pipetting robot molecular biology
UC2 microscopy toolbox microscopy
OpenFlexure microscope microscopy
PocketPCR Thermocycler molecular biology
IORodeo transilluminator Transilluminator molecular biology
FluoPi Fluor imaging gels/plates/colonies/DNA conc molecular biology
FED3 feeding tool for training mice neuroscience
Spikeling in silico neuronal model neuroscience
OpenSpritzer picoliter injection system neuroscience
LED Zappelin’ led controller for visual stimulation neuroscience
Pycontrol behavioural control system neuroscience
PiVR virtual environment for drosophila larvae neuroscience
Ethoscopes experimental rig for invertebrates neuroscience
MouseVR virtual environment for mice neuroscience
Wisconsin photoreactor platform measure photochemical reactions chemistry
Xylotron identify wood products plant science, ecology
AudioMoth acoustic sensor & logger for wildlife ecology
OpenSpim SPIM microsocope developmental biology
Bpod (Sanworks ) microcontroller neuroscience


project contact point use case field
Bonsai-RX reactive software for control of different tools/instruments neuroscience
Deeplabcut neuroscience
The virtual Macaque Brain neuroscience
Simba neuroscience
Stytra neuroscience
DeepLabStream neuroscience
Python (anaconda, jupyter notebook, etc) anything that has datanalysis/code
R anything that has data analysis code
3DµF design microfluidic chips microfluidics

I added links for all of the projects. Let me know if I got any wrong! LOL


oh, wow! Thanks!!
I was a bit lazy to do it in one go, so wanted to slowly fill up with them and more info over the next days…

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Great initiative! Would it be feasible to collect these data in an open spreadsheet for reuse on the go? If not Google Sheet, how about Nextcloud/OpenOffice - shareable/editable sheet or Github? Wasn’t there already a collection of that kind somewhere online? :slight_smile:


I think it would indeed make sense to go beyond a simple list and get a bit more information on these projects. It might be interesting to talk to Bianca Krämer (https://101innovations.wordpress.com/) to see what technology can be used and also discuss the metadata we would like to capture for each project.

any relation to OHO - search engine for sustainable open hardware projects to make ?

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Hi everyone!

Thanks for the suggestions, I really appreciate people taking the time to read things that are posted here and offer suggestions on how to improve things!

having this as an editable spreadsheet is a way to do it, but this here is also an editable wiki post that is formatted in markdown, more open/easy to find than a spreadsheet in a drive somewhere, so I would like to keep it here, or transfer it to a repository somewhere. But repositories come again with the caveat of one needing to know how to work with repositories…

For my use, more than a simple list is not completely necessary. I want to know from people what projects they used and know it works. If people want to add more information, that is also fine!

on another note, can we stop focusing on what technology is used to document this? I would much rather have more useful information being discussed here, like what projects people have used and know are good/mature to make it work in an academic context.

@Jo the only list I know of is the deceased Plos collection, but that is a collection of papers, which unfortunately does not necessarily testify for how mature/usable a project is.


I’d like to share two projects I’ve worked on recently. In both cases we have tried to focus on making the construction process well-documented and straight-forward. Both of these have been constructed and used by multiple research groups at multiple institutions. They are simple tools, which helps with accessibility.

  1. XyloTron
  2. Wisconsin Photoreactor

I’m too shy to add these to your list next to some of the highly polished projects you’ve already collected—I doubt they meet your “mature” metric. Perhaps they are useful as examples from outside of neuroscience though!


You could add 3DuF / (https://3duf.org) - It’s an open-source tool for doing microfluidic design. We are actively looking for contributors and adding more features that simplify the microfluidic device design process.



The Open ‘Whatever’ community is in need of a list of validated/tested or somehow reliable projects. That should clear out researchware - research for the purpose of adding papers with no practical value, abandonware, nevercompletedware, greedware- where projects paid indirectly by public and initially in open space were deleted and taken into private space (like foldoscope).
Unfortunately testing is not free and requires long term commitment.
The other issue is where valuable projects have not been tested or calibrated against industrial instruments.

OHO - search engine for sustainable open hardware projects seems to have this as a mission yet it’s in a very early phase and I see little or no Bio related projects.



That is great start. OpenTron, OpenFlexure should probably be under general biology lab devices rather than Neuroscience but maybe add another column with comma separated tags that could contain neuroscience if the device could be used in that field.

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Thanks everyone for the inputs!
Please keep 'em coming!

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Just added the AudioMoth acoustic sensor, finally something that’s used outside a lab. :sweat_smile:

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OpenCTD could be included, but it’s been evolving over the years so I’m not sure if it would be considered mature. The next iteration will use a Pt RTD for temperature.



Bpod (Sanworks)

would they count ?

Hi @Juliencolomb,
yes those would be fine! Do you mind editing the table and adding them and their respective information?

@Harold This looks quite good! I would not mind adding it. Do you want to edit the table and add it there?

I think Zotero.org deserves a spot somewhere there