raw2tmap 0.1.1

Convert OME-Zarr files to TMAP format

raw2tmap

Convert OME-Zarr files to TMAP format

Requirements

This software requires 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 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                 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 0 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.

Changelog

Changelog

Authors

SciLifeLab BioImage Informatics Facility (BIIF)

License

MIT