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
Merge ROIs from IMC
Re: Merge ROIs from IMC
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.
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.
Re: Merge ROIs from IMC
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
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