# wsic

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Whole Slide Image (WSI) conversion for brightfield histology images.

Provides a command line interface (CLI) for easy convertion between

formats:

```

Usage: wsic convert [OPTIONS]

  Convert a WSI.

Options:

  -i, --in-path PATH              Path to WSI to read from.

  -o, --out-path PATH             The path to output to.

  -t, --tile-size <INTEGER INTEGER>...

                                  The size of the tiles to write.

  -rt, --read-tile-size <INTEGER INTEGER>...

                                  The size of the tiles to read.

  -w, --workers INTEGER           The number of workers to use.

  -c, --compression [blosc|deflate|jpeg xl|jpeg-ls|jpeg|jpeg2000|lzw|png|webp|zstd]

                                  The compression to use.

  -cl, --compression-level INTEGER

                                  The compression level to use.

  -d, --downsample INTEGER        The downsample factor to use.

  -mpp, --microns-per-pixel <FLOAT FLOAT>...

                                  The microns per pixel to use.

  -ome, --ome / --no-ome          Save with OME-TIFF metadata (OME-TIFF and

                                  NGFF).

  --overwrite / --no-overwrite    Whether to overwrite the output file.

  -to, --timeout FLOAT            Timeout in seconds for reading a tile.

  -W, --writer [auto|jp2|svs|tiff|zarr]

                                  The writer to use. Overrides writer detected

                                  by output file extension.

  -s, --store [dir|ndir|zip|sqlite]

                                  The store to use (zarr/NGFF only). Defaults

                                  to ndir (nested directory).

  -h, --help                      Show this message and exit.

```

![A demonstration of converting a JP2 file to a pyramid

TIFF.](https://github.com/John-P/wsic/raw/main/docs/_static/wsic_convert_demo.gif)

# Getting Started

For basic usage see the documentation page ["How do

I...?"](https://wsic.readthedocs.io/en/latest/how_do_i.html).

# Features

- Reading and writing several container formats.

- Support for a wide range of compression codecs.

- Custom tile size

- Lossless repackaging / transcoding (to zarr/NGFF or TIFF) from:

  - SVS (JPEG compressed)

  - OME-TIFF (single image, JPEG and JPEG2000 (J2K) compressed)

  - Generic Tiled TIFF (JPEG, JPEG2000, and WebP compressed)

  - DICOM WSI (JPEG and JPEG2000 (J2K) compressed)

## Read Container Formats

- [OpenSlide](https://openslide.org/) Formats:

  - Aperio SVS (.svs)

  - Hamamatsu (.vms, .vmu, .ndpi)

  - Leica (.scn)

  - Mirax MRXS (.mrxs)

  - Sakura (.svslide)

  - Trestle (.tif)

  - Ventana (.bif, .tif)

  - Generic tiled TIFF (.tif; DEFLATE, JPEG, and Webp

    compressed)

- Other Tiled TIFFs

  ([tifffile](https://github.com/cgohlke/tifffile) supported

  formats)

  - Tiled with various codecs: e.g. JPEG XL, JPEG 2000, WebP, and zstd.

  - RGB/brightfield [OME-TIFF](https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/).

- [JP2](https://jpeg.org/jpeg2000/) (via

  [glymur](https://glymur.readthedocs.io/en/latest/) and

  [OpenJPEG](https://www.openjpeg.org/))

  - Including Omnyx JP2 files.

- [Zarr](https://zarr.readthedocs.io/en/stable/)

  - Single array.

  - Group of (multiresolution) arrays.

  - [NGFF v0.4](https://ngff.openmicroscopy.org/0.4/index.html).

- [DICOM WSI](https://dicom.nema.org/dicom/dicomwsi/) (via

  [wsidicom](https://github.com/imi-bigpicture/wsidicom))

  - [DICOM VL Whole Slide Image IODs](https://dicom.innolitics.com/ciods/vl-whole-slide-microscopy-image).

## Write Container Formats

- TIFF

  - Generic Tiled / Pyramid TIFF

  - OME-TIFF

  - SVS

- JP2

- Zarr (NGFF v0.4)

- DICOM (.dcm)

# Notes & FAQs

Python on [Windows handles multiprocessing

differenly](https://docs.python.org/2/library/multiprocessing.html#windows)

to POSIX/UNIX-like systems. I suggest using the [Windows Subsystem for

Linux](https://learn.microsoft.com/en-us/windows/wsl/about) on Windows

to ensure that wsic functions correctly and efficiently.

# Other Tools

There are many other great tools in this space. Below are some other

tools for converting WSIs.

1. **[bfconvert](https://www.openmicroscopy.org/bio-formats/downloads/)**

   Part of the Bio-Formats command line tools. Uses bioformats to convert

   from many formats to OME-TIFF.

1. **[biofromats2raw](https://github.com/glencoesoftware/bioformats2raw)**

   Convert from Bio-Formats formats to zarr.

1. **[isyntax2raw](https://github.com/glencoesoftware/isyntax2raw)** Convert from Philips' iSyntax format to a zarr using Philips' SDK.

1. **[wsidicomiser](https://github.com/sectra-medical/wsidicomizer)** Convert OpenSlide images to WSI DICOM.

# Credits

This package was created with

[Cookiecutter](https://github.com/audreyr/cookiecutter) and the

[audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage)

project template.