Merge ROIs from IMC

Looking for ways to analyze your dataset? Need help with a software package?
Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
Post Reply
Seb
Posts: 5
Joined: Thu Aug 01, 2019 6:21 pm

Merge ROIs from IMC

Post by Seb » Thu Aug 01, 2019 6:53 pm

hi all

I'm looking for a way to merge various ROIs to rebuild the original image.
I have mcd files, tiffs and txt files per each ROI, I can't seem to find a way to do that tho

any suggestions would be great, thanks
User avatar
votti
Posts: 23
Joined: Mon Nov 27, 2017 12:46 pm

Re: Merge ROIs from IMC

Post by votti » Fri Aug 02, 2019 8:57 am

Hi,

The ablation coordinates required to do this can be found in the XML embedded in the `.mcd` file.
This gets also extracted as easier parsable`.csv` files when converting `.mcd` files to folders containing `.ome.tiff`s using the `imctools` library.
(`Convert zipped IMC acquisitions to input format` step in the ImcSegmentationPipeline https://github.com/BodenmillerGroup/Imc ... sing.ipynb or using imctools directly: https://github.com/BodenmillerGroup/imc ... cfolder.py).

I have a script how to combine the ROI, show them on the Panorama, show the before/after image... based on this extracted metadata and put it on my TODO list to share it.
Seb
Posts: 5
Joined: Thu Aug 01, 2019 6:21 pm

Re: Merge ROIs from IMC

Post by Seb » Fri Aug 02, 2019 7:52 pm

thank you for the reply.
so, i have the coordinate csv files for most of my mcd files, made by a person in our core, but now I'd like to put them together to analyze spatial relationship using the whole image.
I'm happy to give it a shot but I'm not sure where to start...
thanks
Post Reply