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

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

[Mousq]

Many thanks for this great plugin accompanied by such good usage instructions!

I was able to nicely segment objects in multiple channels across hundreds of images in minutes using the batch tool on the Colocalization Image Creator, I am very grateful!

I have a couple of questions about using the Object Counter for analysis:

I have nuclei outlined as a binary element (validated with greyscale element) in output channel 1, binary elements of telomere and DNA damage puncta stains in different colours in output channel 2, and a binary element of co-localisation for these two stains in output channel 3.

In each image, I would like to treat each nucleus as an independent object and count the number of objects within each area outlined/masked i.e. for each nucleus there would be 3 category counts - telomeres, damage, and co-localisation. I would then like to batch process all the images.

Manually drawing round a nucleus I have already defined, setting inclusion region, and counting multipoints for each category, then repeating ad nauseam is not something I look forward to. Is there a way to A) set independent nucleus object ROIs, and B) batch process the counts?

Cheers!

[laurashankman]

Thank you for such a detailed explanation of this plugin. I will need to optimize my nuclear segmentation (my 10um tissue slices can be very densely population) but my main question is about the counter (part II). We count atherosclerotic lesions and sometimes we like to exclude regions from counting and/or look at hyperlocalized regions. Does the contouring feature of the counter accomplish this? Or is there another method you would recommend? When hand counting we visually exclude regions, but I am trying to figure out how to incorporate into this workflow.

[anlu]

UPDATE 1.2.0: You can now control the plugin with ImageJ Macros. Update to latest version to learn more.

[damienvr]

Hello,
I am trying to incorporate this imagej plugin into an fiji macro, in order to apply it to a large batch of images.
But since I can't operate on multi channel images well with a macro, I have to run the commmand Split... The plugin does not work well on single channel images, however. How can I make this plugin work on two single channel images (instead of a single image with two channels)? Or alternatively, how can I call this plugin from inside a macro without splitting the channels?

Thank you!

[danielmekonnen]

Hi, Anders, thank you very much for this very important image analysis plugin. I was tried to add the plugin to FIJI but it says the link is not updated. Could you please help me how to add this plugin to my FIJI software? my image is stained with zihel Neelsen staining and Sudan black My plan is to count/enumerate the Mycobacterium tuberculosis cells that has no lipid droplet, that has 1-2 lipid droplets, and that has >3 lipid droplets. So that I will calculate the mean Lipid droplet content of each bacteria isolated from patients. Thank you inadvance

[ikhmalsyuqkin]

Hi, I'm a student at Imperial College London and I would love to cite your paper in my project but just to confirm whether my images could be analysed using your pipeline, could i send you a few of my images to your email? My acquired images are overlapped (2 channels) and and the intensity is not quite uniform :(