Collection of software used in the lab, as well as free-open source software (FOSS) and free alternatives to commonly used software
Things that were developed and employed in the lab, which might be useful to others
3D print and build your own lab equipment! Links and resources to everything OpenLabware
- 2P microscopy - Non-Telecentric 2P microscopy for 3D random access mesoscale imaging at single cell resolution. Repository.
- 3D printed manipulator - Parametric 3 axis manipulator for use in a laboratory setting, with all files + insturctions for replication.
- 3D printed pipettes - Customisable, high precision pipette, with all files + intstructions for replication.
- 3D priting and electronics - Repository for various 3D printed equipment and DIY electronics for and by the lab.
- FlyPi - The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans. Repository.
- In silico neuron model - Spikeling: A low-cost, Arduino-based hardware implementation of a spiking neuron for neuroscience teaching and outreach. Repository
- LED controller - LED Zapplin': An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging. Repository
- Natural imaging - A low-cost hyperspectral scanner for natural imaging and the study of animal colour above and under water. Repository.
- Open visual stimulator - An open source arbitrary-spectrum spatial visual stimulator for vision research.
- Pressure-injection system - Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes. Repository.
- Spatio-chromatic visual stimulator - An arbitrary-spectrum spatial visual simulator for vision research. Can be used with QDSpy. Repository
- Thunderdome - An open source and versatile spatio-chromatic stimulation system for behavioural experiments for and by the lab.
- Zotero - Free, open-source citation manager with syncing, tagging, PDF managmenet, Chrome plugin for archiving, and much more.
- Atom - Lightweight, fully customisable text editor with syntax, plugins, etc.
- Spyder - Fully featured IDE for scientific Python development, loosely inspired by MATLAB's layout. Included with Anaconda.
- VSCodium - An open-sourced, freely-licensed build of Microsoft's VSCode with telemetry disabled, completely without proprietary branding and such.
- In Python
- Statistics with numpy - Basic statistical functions (mainly descriptives) and some statistical testing functions using numpy.
- SciPy - Ubiquitous, practical data analysis library.
- pandas - Ubiquitous data managment and analysis tools.
- QDSpy - Euler lab's software and accompanying Python library for designing and displaying stimuli.
- ImageJ Fiji distribution - Distribution of ImageJ2 for image analysis bundled with many useful plug-ins and extensive documentation.
- scikit-image - Powerful Python library for image processing based on scipy.ndimage.
- OpenCV imgproc. - OpenCV's library for image processing.
- scikit-learn - Predictive data analysis and modelling tools for Python built on numpy, SciPy, and Matplotlib.
- In Python
- Pingouin - Advanced but easy-to-use, open-source, Python library for statistical testing and analysis.
- scikit-posthocs - python library which provides post-hoc testing, primarily using DataFrames from pandas.
- statannot - Simple and effective way to add stats bars to Seaborn figures (may work with Matplotlib, with in-built stats test or by passing own P-values.
- GNU Octave - MATLAB-equivalent scientific programming language with familiar GUI and largely compatible with MATLAB scripts and functions
- JASP - SPSS-like software featuring classic and Bayesian analysis.
- Jamovi - SPSS-like, software for basic analysis, with simple plotting tools.
- Julia - Fully fledged, general-purpose programming language well-suited for data analysis and computational stuff.
- R - Coding environment geared towards statistical computing and graphing with familiar GUI and largely compatible with MATLAB scripts and functions.
- Tabula - Tool for extracting tabled data from PDFs (requires Java to run locally).
- WebPlotDigitizer - Relatively easy-to-use tool for extracting data points from most images. Currently does not allow PDF import for Windows, but screenshots can be pasted directly. Online version.
- In Python
- matplotlib - Comprehensive library for data visualisation.
- seaborn - Data visualisation library based on matplotlib with better emphasis on aesthetics.
- GNU Octave - Features MATLAB-like plotting functions.
- GIMP - Free, open-source raster graphics editor.
- Unpaywall - Chromium extension which finds legal open/free versions of scientific articles (e.g. in Nature, Science, etc.).
- Joplin - Free, open-source note taking app functionally similar to OneNote. Notes can be written in rich-text editor or Markdown. Synchronisation through various cloud services.
- Simplenote - Similar to Joplin with in-built synchronisation, but somewhat utilitarian (e.g. no rich-text editor).
- SpikeInterface - Unified Python framework enabling spike sorting, analysis pipelines, preprocessing, postprocessing, viusualisation, and more.
- OpenNeuroscience - User-driven databse of open neuroscience projects
- rOpenSci - Collection of various open-source packages for R.
- Foxit Reader - Free, light-weight alternative to Adobe Acrobat Reader with equally powerful annotation tools.