Stress granules quantification

imagej1
analyze-particles
cellprofiler
imagej
plugin
cellprofiler-analyst
#1

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

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#2

Could you please provide an example image?

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#3

Dear Anna,

thank you very much for your response.

I am attaching some images.

Best regards,

Kosi

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#4

Image2.tif (3.0 MB)

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#5

Image2 DAPI.tif (3.0 MB)

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#6

Image2 merge.tif (3.0 MB)

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#7

Image1.tif (3.0 MB)

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#8

Image1 DAPI.tif (3.0 MB)

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#9

Image1 merge.tif (3.0 MB)

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#10

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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#11

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

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#12

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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#13

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

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#14

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

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