Free and open source

A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.

FishFeats: napari plugin to perform quantification of multimodal labeling at the single-cell level in 3D tissues.

FishFeats allows to perform together in the same pipeline several analysis to quantify epithelia cells in 3D tissue, analysing cell morphology, nuclei, immuno-staining or RNA expression. The plugin allows flexibility to let the user choose the relevant step for a specific biological question.

A python package for background and shading correction of optical microscopy images

BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.

Colocalization Colormap –an ImageJ Plugin for the Quantification and Visualization of Colocalized Signals

This ImageJ plugin implements the Jaskolski's algorithm (Jaskolski et al. 2005). It creates a pseudo-color map of correlations between pairs of corresponding pixels in two original input images. With it one can quantitativly visualize colocalization.

This plugin is able to stitch an arbitrary collection or grid of images, it does not matter if it is 2d, 3d, 4d or 5d images as long as all images are of the same type. In contrast to the Pairwise Stitching of two images, this plugins will load (and potentially save) the images from/to harddisc.