Convert OME-Zarr files to TMAP format
Python 3.9 or later
Use the package manager pip to install raw2tmap:
pip install raw2tmap
To enable the --dzi option, install with the dzi extra (requires libvips):
pip install "raw2tmap[dzi]"
To convert an OME-Zarr file to TMAP format:
❯ raw2tmap --help
Usage: raw2tmap [OPTIONS] RAW_FILE_OR_URL TMAP_FILE
Convert OME-Zarr files to TMAP format.
Options:
-t, --time INTEGER RANGE Time index. [x>=0]
-c, --channel INTEGER/TEXT Channel index or name.
-z, --depth INTEGER RANGE Depth (z) index. [x>=0]
--layers DIRECTORY Path to layer images, relative to TMAP_FILE.
Defaults to '.{TMAP_FILE}/layers'.
--compression ALGORITHM Compression algorithm. [default: none]
--tilesize INTEGER RANGE Tile size in pixels. [default: 256; x>0]
--format [0.1|0.2|0.3|0.4] OME-Zarr format version. [default: 0.4]
--dzi Write DZI file (requires pyvips).
-q, --quiet Quiet mode (hide progress bar).
--version Show the version and exit.
--help Show this message and exit.
Example:
raw2tmap -t 0 -z 10 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr 5514375.tmap
OME-Zarr files can for example be created using bioformats2raw.
If you find a bug, please raise an issue.
Pull requests are welcome.
For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.