How to create multiple ROI from a same image using create selection

Hello everyone,

I am quite new on Fiji and i am trying to quantify aggregates in my cells. i have an image on which i have set an automatic threshold as seen on the image 1 here. using create selection and make it inverse to be able to surround the perimeter of the different cells (image 1). however i dont know how to save each cell as a separate ROI as after i want to quantify aggregates respectively in each cell see image 2.

can anyone help me with this please!
by the way if any of you think that is not the right method to quantify the aggregates i am very willing to have some feedbacks.

Thanks a lot in advance,
Best
Elise


@eliu

Instead of Create Selection, which selects all non-zero pixels and considers it a single region/object, you’ll want to use Analyze Particles, which considers each object unique/separate. Using this tool - you can also filter out those really small ‘objects’ that you are picking up in Create Selection. These ROIs can then be saved in the ROI Manager and then overlaid on other channels/images.

If you have more specific questions again - just ask. We are here to help.

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Hi @etadobson,

Thank you a lot for your quick answer. so i have followed your advice and used Analyze Particles . the tool is very interesting but i think i am bad a it because now that i have generate the ROI i cannot add them to my ROI manager. how should I do this ?
I have also tried to copy it and past it on another channel but then it just replaces the image rather than copying the ROI.

Thank you in advance,
Best
Elise

@eliu

No worries. I’ll point you to the resources that show the exact steps to take:

Going through the segmentation workshop video linked below^^ should help you - a lot. The exact steps for what you want to do are demoed starting at 1:22:06. :slight_smile:

Here are some helpful links as well that you might find useful:

@etadobson

Thank you very much for your answer!
All these links are definitely going be very helpful/useful, i will go through everything very carefully. :slight_smile:
best

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If you have more questions - just ask. We are here to help.

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