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afw

afw_testdata

augmend

simple package for augmentation of n-dimensional arrays

automatedmicroscopy

cecog

A fast and cross-platform image analysis framework for fluorescence time-lapse microscopy and bioimage informatics.

cellprofiler

CellProfiler is open-source cellular image analysis software.

ch.psi.imagej.hdf5

ImageJ HDF5 Plugin

commmicroscope

Fiji code to read-write registry and run macro on new files of directory

confocalgn

Generates simulated confocal data from a ground truth signal

cytosim

Cytosim is a cytoskeleton simulation engine

dotlinker

linking segmented dots

embldl2022

fcsfiles

Read fluorescence correlation spectroscopy (FCS) data files. Forked from https://pypi.org/project/fcsfiles

fiji-plugin-cats

glcm2

calculates GLCM, to make it friendly for scripting.

list-of-update-sites

The update sites ImageJ knows about automatically

microscoperemotecontrol

About Microscope Remote Control is an application to control a microscope remotely via network

minflux-analysis

Some tools to work with Minflux microscopy data

mypic

npc_assembly_otsuka_2022

Code associated to the publication "A quantitative map of nuclear pore assembly reveals two distinct mechanisms" Otsuka et al. 2022, Nature.

stardist

StarDist - Object Detection with Star-convex Shapes

teaching-dl-course-2022

Materials for the EMBL Deep Learning course

training-resources

Resources for teaching/preparing to teach bioimage analysis

tutorials

ImageJ programming examples

visiview-scripts

A collection of macros for the VisiView acquisition software