adapting to TIff images multiplex (4i)

[Nal44]

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]

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]

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]

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]

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