glencoesoftware/bioformats2raw

How TIFF stack To OME-zarr

Opened this issue · 2 comments

Iamlearn commented

please, How to convert TB size TIFF stack into OME-zarr

melissalinkert commented

To convert a TIFF file to OME-Zarr/OME-NGFF:

  • download the latest bioformats2raw-*.zip from https://github.com/glencoesoftware/bioformats2raw/releases and unzip it
  • from the bin directory that was extracted from the zip, run bioformats2raw /path/to/file.tiff /path/to/ome.zarr
    • replace /path/to/file.tiff with the path to your TIFF file, and replace /path/to/ome.zarr with the path to write converted data

https://github.com/glencoesoftware/bioformats2raw?tab=readme-ov-file#usage documents the different options that can be used to convert. We recommend starting with the defaults unless you know that you need something different.

If you see an error message when running the conversion, please tell us the exact error message. If the converted OME-Zarr is not what you expect, please tell us as many details as possible so that we can suggest a solution.

Iamlearn commented

I want to convert two-dimensional sequence diagrams one by one into ome-zarr.Due to the large amount of data, the input can only be sequence diagrams, as shown in the following figure.The total size is 40000x40000x15000 16Bits,Each sheet has a size of 40000x40000, and there are 15000 public sheets available.
image