Using aggrecount for stress granule quantification

Hi everyone,

I wanted to ask if anyone was familiar with the imageJ plugin Aggrecount and how to use it? I have been playing with it on Fiji but am having trouble completing and moving past the “setup” stage where aggrecount constantly asks me questions about an image and to set up threshold values. My image looks like this and is coming out like this, but I only want to quantify the stress granules.

Thank you so much!

Hi @bd6376
have you checked the instructions here https://github.com/AggreCount/AggreCount/tree/master/AggreCount_download/documentation

Hi Peter, yes I have! When I do the setup process, the program just stops following me through steps at some point and I never actually get to the part where these granules are quantified. When it asks for different “channels” for nuclei and granules, I feel like I haven’t been doing the right thing, mainly using laso just to highlight whatever it asks for. Let me know what you think

Use the test images from the GitHub page for your first tests.
They are 2-channel 16-bit.

Your images are 1-channel RGB.

You should correct this.

In addition, if you are working with ImageJ1 you have to install the CLAHE plugin.
(https://imagej.net/Enhance_Local_Contrast_(CLAHE))

I think in FIJI it is installed per default.

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Hi,

Thank you so much for your help! I was looking through the test images on GitHub and they all seem like the same image, am I looking at the right thing?

It seems not.
There are 5 different images.

Anyway, for your test you only need one of them.
Use one of the images to make sure that the macro is running as expected and that you have an understanding of its principle, options and settings.

Hi,

Peter is correct in that you need to have your channels for nuclei and stress granules separate (IE not RGB images) for AggreCount to be able to quantify the stress granules. Let me know if you have any issues! I’m happy to help.

-Jacob