Useful Links

This is a very brief compilation of links to web resources we have found useful or relevant to our work. The resources are maintained by their respective owners and/or webmasters and NOBIC assumes no responsibility for the functionality of the links and/or the contents of the resources. The resources in the Open Source Hardware and Software category are ordered alphabetically and the lists do not attempt to be in any way complete or exhaustive.

Biophotonics Imaging Laboratory - COMI
Cellpose - a generalist algorithm for cellular segmentation
CellProfiler
cellSTORM 2 - a low-cost super-resolution imaging device
BioImage Informatics Index - a database of image analysis tools
The fairSIM project
Fiji
Fee-Scopes - lightweight head-mounted microscopes primarily for birds
FLIMfit - TCSPC data fitting
Hohlbein Lab Open Microscopy Directory - Probably the most extensive listing of open-source resources for microscopy
ilastik - the interactive learning and segmentation toolkit
ITOM - laboratory automation suite
JIPipe - visual programming for ImageJ
Label Studio - data labeling platform
Making the Most of Your Microscope - resources for 3D printing of microscopy accessories
µCube - a framework for 3D printed optomechanics
μManager - probably the best-known open source microscope control software
mesoSPIM
MINI2P_toolbox - a miniature head-mounted 2-photon microscope for small animals and other resources from Kavli Institute for Systems Neuroscience
MicroscoPy - open source microscope
MSSR - super-resolution plugin for FIJI
napari - Multi-dimensional image viewer for python
NINscope - a miniature head-mounted microscope for small animals
OpenFlexure Microscope
OpenSPIM
Optical Cell Biology Laboratory - open source image analysis tools including ZeroCostDL4Mic
PgFocus - hardware autofocus
Puma - 3D Printed Microscope
QuPath - Open Software for Bioimage Analysis
Refractive Index Imaging - software libraries for refractive index imaging in 2D and in 3D
Ries pieces - recipes for open microscopy
scikit-image - image processing in Python
SIMToolbox
SegmentAnything Model
Squid: Simplifying Quantitative Imaging Development and Deployment (contains an extensive list of other open-source projects)
StarDist - trainebale segmentation
UC2 - Open and Modular Optical Toolbox
UCLA Miniscope - a miniaturised head-mounted microscope for small animals
UNAL-Optodigital - Digital Lens-less Holographic Microscopy hardware and ImageJ plugins
Vicidomini Lab Repositories
Yide Zhang Lab Repositories
YouScope - Microscope Control Software

Microscopy Australia MyScope
iBiology Microscopy Course
Microscopy Primer
Global BioImaging Virtual Training Platform
Introduction to Bioimage Analysis by Pete Bankhead
Bioimage Data Analysis Workflows - Open Access Textbook
YouTube Channel of Live Cell Imaging Core Facility at Karolinska Institutet
RMS Python for Bioimage Analysis Course
Optics Course at MIT

Microforum - Light microscopy forum
Image.sc - Forum for users of open access image analysis and microscope control software

BioImage Archive - An extensive collection of bio-imaging datasets linked to published research
BioImage Model Zoo - Advanced AI models in one-click
Brillouin Scattering Database - A small database of Brillouin spectra of mostly simple compounds
FluoroFinder - Fluorophores database, spectra viewer etc., requires registration to use
FPbase - A fluorophore spectra viewer with an extesive database of fluorophores, optical filters etc., a databse of fluorescent proteins
MicrobioRaman - A database of microorganism Raman datasets
Openanalysis.org - Resources for microplastic research by Moore Institute for Plastic Pollution Research, including Open Specy, a tool for Raman and FTIR spectra identification
Opticalmaterials.org - AI-generated database of optical properties
Raman base - "The Ultimate Raman Spectroscopic Database" according to its developers
RefractiveIndex.INFO - A Database of optical properties of materials
Spectra Viewer - A database and a viewer of fluorophore and optical filter spectra

SingaScope - A Singapore-Wide Microscopy Infrastructure Network
Imaging Southeast Asia (iSEA) - SingaScope on a broader scale
Global BioImaging - SingaScope on a yet broader scale
BioBrillouin Society
Royal Microscopical Society
AI4Life - an infrastructure to support life scientists in the adoption of machine learning solutions
GloBIAS - Global BioImage Analysts' Society
neubias - Network of european bioimage analysts
COBA - The Centre for Open Bioimage Analysis
Globals - Software for data anlysis in fluorescence correlation spectroscopies, time-resolved fluorescence etc. by Enrico Gratton
LensNet - Lens design starting point generator analysts