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niaid / sitk-ibex

Aligning images acquired with the IBEX microscopy imaging technique
Apache License 2.0
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adapting to TIff images multiplex (4i) #50

Open Nal44 opened 11 months ago

Nal44 commented 11 months ago

Hi,

I understand how the code works and how to install ect.

I want to use this code on 4i multiplex images (similar to IBEX), my images are in TIF, so I have a few questions :

In the code example below how do I adapt the code to run my images ? I have a fix image (dapi) and 20 or more channels that needs registration. But for a .Tif images , how / where to add the images ? is there a specific folder or just add all to the root (need a specific tree )? My images are single channel so how to proceed something like --affine "LiverDAPI" "Liverxyz" ? Then, I don't understand the tx_p2_to_p1.txt ?For .TIF images is it necessary ?

Thanks a lot,

python -m sitkibex registration --affine "spleen_panel2.nrrd@CD4 AF594" "spleen_panel1.nrrd@CD4 AF594" tx_p2_to_p1.txt python -m sitkibex registration --affine "spleen_panel2.nrrd@CD4 AF594" "spleen_panel3.nrrd@CD4 AF594" tx_p2_to_p3.txt

blowekamp commented 11 months ago

Are you able to convert the image to OME-NGFF/ZARR with a tool like bioformats2raw?

Further details are provided here: https://github.com/niaid/sitk-ibex#additional-example

Nal44 commented 11 months ago

Hi, Worth a try, my images are .LIF (from a Leica microscope) , so I will to do convert them and see how it goes. The "omerta" metadata that are mentioned are the txt files I presume? thanks !

blowekamp commented 11 months ago

The omera XML data will be in a subdirectory named "OME" in the zarr directory. This is the same information that ImageJ/FIJI can display when importing files with bio formats.

Nal44 commented 11 months ago

ok got it thanks, will send updates as it goes.

can I do rigid registration as well ? I want to compare affine VS rigid since I have some rotation and local deformations. Any suggestions to solve that are welcome :) ,thx