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SchmollerLab / Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
BSD 3-Clause "New" or "Revised" License
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Request for enabling some features for 3D segmentation #209

Open ArohiKhurana opened 1 year ago

ArohiKhurana commented 1 year ago

Description:

I have the following suggestions-

  1. Enabling of Custom annotation option in 3d segmentation module.
  2. Enabling of remove from ananlysis option in 3d segmentation module.
  3. Also, it would be great if colocalization of signals coming from 2 different channels is also an output in the excel sheet at the end. It could be that it's already available and I am just not aware of it. In anycase just let me know.

Thanks a lot!

ElpadoCan commented 1 year ago

Hi Arohi,

I can definitely implement what you are asking. However, I have a question, how would you want to quantify colocalization?

Because you can already load multiple fluorescent channels and compute measurements of each channel but there is nothing specific for colocalization since there isn't a single universal metric for that.

Since you can define custom measurements in a variety of ways, as soon as you know how you want to quantify colocalization I can help you implementing this custom measurement. Let me know, thanks!

Cheers Francesco

ArohiKhurana commented 1 year ago

To explain the exact situation, I am currently staining histones in one channel and nuclear DNA in another channel. I would like to know what percentage of histone signal is overlapping with the nuclear signal and what percent is outside the nucleus because I am seeing histone signal throughout the cell (eventhough I can also clearly qualitatively identify the nuclear histone signal in many cells). This is why I was thinking if I could actually quantify the nucelar histone signal vs the cytoplasmic histone signal.

ElpadoCan commented 1 year ago

That is definitely possible, but there are multiple ways to do this. One way is to segment nuclear signal and histone signals separately and then compute the area overlap. Another option is to compute some kind of ratio between the means of the two signals or some other quantile or effect size. All of this is already possible within Cell-ACDC.

You can for example define a custom measurement from the Measurements menu on the top menu bar of the GUI, or you can define custom measurements between different segmentation masks from the Utilities --> Measurements menu on the top menu bar of the little cell acdc launcher.

Let me know what strategy you want to try first, thanks!

Cheers Francesco

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