This repository contains the files used to test OME-TIFF images for BIDS-microscopy. The NDPI and the OME-TIFF test images are respectively sample data from OME downloads (https://downloads.openmicroscopy.org/images/Hamamatsu-NDPI/manuel/) and documentation (https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/data.html). These images have been used under Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). No change was made to the original images.
The following procedure describes how to install the Python packages used for the ometiff-tests notebook. These packages are useful to read, write OME-TIFF and convert different types of file to OME-TIFF.
- Open the Anaconda Prompt
- Type in the following line :
pip install tifffile - The documentation relative to this package can be found here: https://github.com/cgohlke/tifffile
- Open the Anaconda Prompt
- Type in the following line :
pip install pyvips - pyvips is the Python binding for libvips. The documentation can be found here: https://libvips.github.io/pyvips/index.html
- Download the file vips-dev-w64-web-X.Y.Z.zip from the latest release here: https://github.com/libvips/build-win64-mxe/releases
- Extract the .zip file somewhere on your Local Disk (C:). You should get the folder vips-dev-X.Y, where X.Y is the release version (ex: 8.11).
- Open the Python file you’re working on in your code editor (ex: VS Code)
- For tifffile, simply incorporate
import tifffilein your code - For libvips, add the lines:
from ctypes import *
cdll.LoadLibrary("C:/.../vips-dev-X.Y/bin/libgobject-2.0-0.dll")
cdll.LoadLibrary("C:/.../vips-dev-X.Y/bin/libvips-42.dll")
import pyvips
Where C:/.../vips-dev-X.Y represents the path to where you saved the previous folder (see above). Without the three lines before import pyvips, you may get an OSError because the libraries can’t be found.
Tested with Visual Studio Code 1.57.1 with Python 3.9.2 on Windows10