Tool for converting WSIs from Olympus' cellSens VSI to Generic TIFF.
A simple Jupyter Notebook can be seen here demonstrating how use the tool.
To run the tool, you need to configure bftools and vips. To do that, follow the instructions below for the operating system of interest:
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Download bftools (click here)
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Install vips and JDK
sudo apt update
sudo apt-get install openjdk-8-jdk
sudo apt install libvips-tools
Install from source:
pip install git+https://github.com/andreped/vsi2tif
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] [-p PLANE] [-q QUALITY] [-m MAX_MEM] [-v VERBOSE]
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
-s TILESIZE, --tilesize TILESIZE
tile size to use during both conversion steps
-p PLANE, --plane PLANE
which image plane to convert image from
-q QUALITY, --quality QUALITY
compression quality used with JPEG compression
-m MAX_MEM, --max-mem MAX_MEM
set maximum memory in the java vm
-v VERBOSE, --verbose VERBOSE
set verbosity level
This project has MIT license.