details of input files for stitching workflow

[piotrsan]

Hello,

I need help to convert Zeiss czi files to TIFF for input into the pipeline. I am not sure what TIFF file format to use and what name convention, if any, is needed for the pipeline to properly recognize the files.

Could you also provide the details of what is to be included in the ImageList.csv file and/or what tool could be used to generate this, is available?

Thanks,

best,

Piero

[lillvis]

Hi Piero,

I would recommend trying to stitch Zeiss light sheet-data using the Saalfeld lab Z1 stitching code: https://github.com/saalfeldlab/stitching-spark. This was method is similar to what we have done for the lattice light-sheet data and was integrated into Nextflow workflows via the EASI-FISH data analysis pipeline (https://github.com/JaneliaSciComp/multifish).

However, if you want to try to convert from czi to TIFF and use our stitching pipeline, here are the details.

The TIFF files are baseline TIFF. The naming convention is as follows: Scan_Iter_0000_CamB_ch0_stack0000_642nm_0000000msec_0509746154msecAbs_013x_027y_001z_0000t.tif, Scan_Iter_0000_CamB_ch1_stack0000_560nm_0000000msec_0509746154msecAbs_013x_027y_001z_0000t.tif, Scan_Iter_0000_CamA_ch2_stack0000_488nm_0000000msec_0509746154msecAbs_013x_027y_001z_0000t.tif. However, it is not necessary to use this naming convention.

The ImageList.csv file includes this information in separate columns:
Filepath, Filename, Stage X (um), Stage Y (um), Stage Z (um), Objective X (um), Objective Y (um), Objective Z (um).

I've attached an example of this image list. We have not created a tool to generate this ImageList.csv file as it is generated automatically by the lattice light-sheet software. Hopefully, the stage and objective position metadata is present for each czi file so that this ImageList.csv file can be generated.

If you decide to give this approach a shot, please let us know how it goes.

BEST,
Josh

ImageList_example.csv