raw2tmap

Convert OME-Zarr files to TMAP format

Requirements

Python 3.9 or later

Installation

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]"

Usage

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.

Support

If you find a bug, please raise an issue.

Contributing

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.

Changelog

Changelog

Authors

SciLifeLab BioImage Informatics Facility (BIIF)

License

MIT