ImageJ plugin: Semi-automatic cell counting (with colocalization / categorization). Object based.

new ImageJ plugin: A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis

Link to paper: https://www.nature.com/articles/s4159...

Video explanation (part 1):    • ImageJ/FIJI plugin: Semi-automatic cell-by...  
Video explanation (part 2):    • ImageJ plugin: Semi-automatic cell countin...  

FIJI update site: https://sites.imagej.net/ObjectColoca...

Features:

ImageJ plugin 1: Colocalization Image Creator:
*Pre-process multichannel Z-stack (or 2D) microscopy images into a visual format for faster, simpler, and more accurate colocalization analysis.
*Designed to help avoid common colocalization analysis artifacts and errors.
*Can transform Z-stack 3D data into a specialized 2D Z-projection where Z-projection colocalization artifacts are removed/reduced. This simplifies the analysis of 3D colocalization data.

ImageJ plugin 2: Colocalization Object Counter:
*Quantity (count) cells/objects in a semi-automatic manner.
*Assign, classify and keep track of multichannel signal presence/absence (colocalization analysis) for each cell/object.
*Tools for subsequent 3D modeling/representation of data: draw tissue contours and indicate image-series global XY-origin.
*Save data, load data, and export data to Excel.

Custom Excel macro-file:
*Import data from Colocalization Object Counter
*Analyze and edit data from image series.
*Export combined image series data to Matlab for 3D modeling

Custom Matlab script:
*3D visualize cells according to colocalization data
*3D visualize tissue contours


I hope the community will appreciate our work. The ImageJ plugin 1 might be somewhat hard to understand how to use effectively (though we hope not), but ImageJ plugin 2 should be very simple and useful to the broader community. I found a good cell counting tool for ImageJ lacking, so maybe this plugin (and the other) can be included as a standard part of FIJI.

Sincerely,
Anders Lunde, PhD
University of Oslo, Norway