Python tool that converts TIFF files, using the tifffile package, to an
intermediary raw format.
WARNING: This package is EXPERIMENTAL and is not meant to be an
alternative to bioformats2raw for TIFF files. ALL metadata present
in the input TIFF file is currently lost. ALL pixel data present
in the original TIFF file is loaded into RAM.
- Python 3.5+
Basic usage is:
tiff2raw write_tiles /path/to/input.tiff /path/to/tile/directory
Please see tiff2raw write_tiles --help for detailed information.
Output tile width and height can optionally be specified; default values are
detailed in --help.
A directory structure containing the pyramid tiles at all resolutions and macro/label images will be created. Be mindful of available disk space and available RAM, as larger TIFF files can result in >20 GB of tiles and require GBs of free RAM.
Use of a n5 (the default) or zarr --file_type will result in losslessly
compressed output. These are the only formats that are currently
supported by the downstream raw2ometiff.
This package is highly sensitive to underlying hardware as well as the following configuration options:
--max_workers--tile_width--tile_height--batch_size
On systems with significant I/O bandwidth, particularly SATA or NVMe based storage, we have found sharply diminishing returns with worker counts > 4. There are significant performance gains to be had utilizing larger tile sizes but be mindful of the consequences on the downstream workflow. You may find increasing the batch size on systems with very high single core performance to give modest performance gains.
In general, expect to need to tune the above settings and measure relative performance.
The TIFF converter is distributed under the terms of the GPL license.
Please see LICENSE.txt for further details.