imagej / imagej/imagej2

Pluggin segmenting less number of particles using ImageJ version 1.53f

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Description

I am trying to use the same pluggin/method that was used in an old version of imageJ and compare it to the current ImageJ version.
So for comparison purposes, I extracted organisms from the same picture, and the segmentation of images using the same pluggin produces much fewer silhouettes (<25%) with the recent version of ImageJ (1.53f) than when using an older version of ImageJ (1.1).
I have tried, but it did not work, to troubleshoot imageJ according to the indication in the website: https://imagej.net/Troubleshooting.html#The_same_plugin_gives_different_results_on_different_machines.21

It seems that the current version of ImageJ Analyze of particles is not working properly and only detecting particles with a smaller area 0.049-5.64mm. Even when I select the option of 0-infinity in the current ImageJ version, I obtain much smaller size organisms (0.00010 -5.69mm) for the same image. While using an old version of ImageJ (1.1) for the same image it was detecting particles from 0.049 to 20.26mm.

Is there anything I can do to add to the pluggin to make sure that the data are replicated, i.e. the extraction of particles is constant and does not vary with the ImageJ version?
Or is there something else that could be affecting this?
Thanks in advance.

![image](https://user-images.githubusercontent.com/3626621/102354132-0e2cc900-3fa2-11eb-85ee-75ca68571d19.png) The image attached shows the position of the animals detected using the old version- of imageJ 1.1 (black colour) and new version 1.53f- (red colour). Y-axis indicates the position of particle detected over the y axis in the digitized image and X-axis indicates the position of the particle detected in the x-axis in the digitized image.

Contributor guide

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Research direction

Start by reproducing the reported Analyze Particles results with the same image and settings in ImageJ 1.1 and 1.53f, using the linked troubleshooting guidance. Compare the detected particle ranges and silhouettes shown in the attached image; done means identifying why the versions differ or documenting a reproducible compatibility issue.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
computer-vision
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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