Links
Inside the University
Free/Opensource Software
Matlab Geometry, a very comprehensive sets of functions to handle basic 2D/3D geometry
ZeroCostDeepLearning4Microscopy, ready to use deep learning cell imaging tools
BioImageXD, for visualizing images, especially 3D image stacks
CellProfiler, for image analysis of cell phenotypes.
ImageVis3D, for visualizing 3D data on both desktop and mobile devices
BigDataViewer, a Fiji plugin for visualizing 3D data
tTt and qTfy, for cell tracking and analyzing
CT-FIRE, for fiber extraction such as in collagen matrix
EPFL biomedical imaging group, multiple image analysis plugins
Other useful resources
Data visualization practical guide
Statistical analysis practical guide
A few high lighted imaging techniques from Hamamatsu