A package for converting images from cellSens VSI format to tiled, pyramidal TIFF
Project description
vsi2tif
Tool for converting WSIs from Olympus' cellSens VSI to Generic TIFF.
To quickly get started, see these notebooks (Ubuntu Linux, macOS) for installing the tool, converting your first image, and verifying that the image works with OpenSlide.
Continuous integration
Build Type | Status |
---|---|
Integration Tests | |
Unit Tests | |
Linting Checks |
Requirements
To run the tool, you need to configure bftools and vips. To do that, follow the instructions below for the operating system of interest:
Ubuntu
-
Download bftools (click here)
-
Install vips and JDK
sudo apt update
sudo apt-get install openjdk-8-jdk
sudo apt install libvips-tools
macOS
-
Download bftools (click here)
-
Install vips and JDK
brew install --cask zulu@8
brew install vips
Windows
To install bftools and vips, I recommend using Powershell as much as possible to automate the installation steps.
https://github.com/libvips/build-win64-mxe/releases/download/v8.15.3/vips-dev-w64-all-8.15.3.zip
- Uncompress downloaded file and place it at an appropriate place, like at home
unzip ~/Downloads/vips-dev-w64-all-8.15.3.zip
mv ~/Downloads/vips-dev-w64-all-8.15.3/vips-dev-8.15/ ~/vips-dev-8.15/
- Add path to
vips.exe
to the PATH (requires powershell administrator)
$Env:PATH += ";$HOME/vips-dev-8.15/bin/"
Installation
Install from PyPI:
pip install vsi2tif
Alternatively, install from source:
pip install git+https://github.com/andreped/vsi2tif
Usage
The conversion tool is available through a command line interface (CLI).
Example for converting a single WSI:
vsi2tif -i /path/to/olympus/image.vsi -o /path/to/converted/image.tif -b /path/to/bftools/bfconvert
Here is an example to perform batch conversion of a folder of WSIs:
vsi2tif -i /path/to/olympus/wsis/ -o /path/to/converted/wsis/directory/ -b /path/to/bftools/bfconvert
Comprehensive CLI documentation can be seen below:
usage: vsi2tif [-h] -i INPUT -o OUTPUT -b BFCONVERT [-c COMPRESSION] [-s TILESIZE] [-q QUALITY] [-m MAX_MEM] [-v VERBOSE] [--remove-name-spaces] [-p PLANE]
vsi2tif - simple tool for converting images from cellSens VSI to Generic TIFF
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
folder with input files
-o OUTPUT, --output OUTPUT
folder for output files
-b BFCONVERT, --bfconvert BFCONVERT
path to bfconvert tool
-c COMPRESSION, --compression COMPRESSION
compression technique for final image - default 'jpeg'
-s TILESIZE, --tilesize TILESIZE
tile size to use during both conversion steps - default 1024
-q QUALITY, --quality QUALITY
compression quality used with JPEG compression - default 87
-m MAX_MEM, --max-mem MAX_MEM
set maximum memory in the java vm - default 32
-v VERBOSE, --verbose VERBOSE
set verbosity level - default 1
--remove-name-spaces replace spaces in filename with underscores in batch mode
-p PLANE, --plane PLANE
which image plane to convert image from. If set to -1, all series are converted and the largest is kept - default 0
License
This project has MIT license.
How to cite
If you found this tool useful in your research, please cite the following:
@software{pedersen2024vsi2tif,
author = {André Pedersen and David Bouget and Sebastian Krossa and Erik Smistad},
title = {{andreped/vsi2tif: v0.1.4}},
month = sep,
year = 2024,
publisher = {Zenodo},
version = {v0.1.4},
doi = {10.5281/zenodo.13745169},
url = {https://doi.org/10.5281/zenodo.13745169}
}
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