Stress granules quantification

Dear all,

I would like to ask which program is the best to quantify stress granules.

Thank you very much in advance.

Best regards,

Kosi

Could you please provide an example image?

Dear Anna,

thank you very much for your response.

I am attaching some images.

Best regards,

Kosi

Image2.tif (3.0 MB)

Image2 DAPI.tif (3.0 MB)

Image2 merge.tif (3.0 MB)

Image1.tif (3.0 MB)

Image1 DAPI.tif (3.0 MB)

Image1 merge.tif (3.0 MB)

Gorgeous! I suggest you download the example Speckle Counting pipeline on CellProfiler’s examples page: https://cellprofiler.org/examples/#speckle-counting

You will want to adapt it by adding an IdentifySecondary module to identify the cytoplasm region of each cell so that the speckles can be associated with those areas (whereas the example pipeline associates speckles with the nuclei).

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Unfortunately an error message appears “Could not find pipeline file: sn_0_606356.”

When you start CellProfiler, sometimes you get that message (post). You can ignore it and load the pipeline file as described in the Welcome screen.

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Thank you very much! I started it but I got a bit lost. Could you please guide me through?

Dear Kosi,
if you are more familiar with ImageJ/Fiji you could also try the particle detector within MiToBo which was originally also designed to detect stress granules. Just activate the “MiToBo” update site within Fiji, then run the “MiToBo Runner” from the plugins menu and search for the entry “ParticleDetectorUWT2D”. On running the operator you will get a window where you can specify your input image, an optional exclude mask, and some other parameters effecting the scale of particles to be detected and the sensitivity of the detector. Playing around a bit with the parameter settings should allow you to extract your stress granules with good quality.

Cheers,

Birgit

Dear Birgit,

thank you very much for your reply! I faced only one small problem. I run “MiToBo Runner” but I could not find “ParticleDetectorUWT2D”. I am attaching a screenshot from the message that appears.

Could you please help me figure this out?

Thank you very much in advance.

Best regards,

Kosi

I forgot to mention that I used ImageJ for MiToBo Runner.

Dear Kosi,
using ImageJ should not cause problems. However, you seem to run ImageJ with a Java version < 1.8, since Java 1.8 refers to version 52.0 which your Java virtual machine does not support. MiToBo requires at least Java 1.8 to run properly, so probably you need to update your Java installation.

Cheers,

Birgit

Hi Kosi

I quickly just created a simple pipeline to identify the nucleus


Identify the granules

And associate them to each cell

Best
Lee

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Speckles.cpproj (656.8 KB)