pyramid_creator

This script is used to convert regular OME-TIFF files (exported from Zeiss ZEN for example) into pyramidal OME-TIFF ready to use in QuPath (see more information here).

It uses either QuPath in console mode (eg. without graphical user interface), calling the bundled createPyramids.groovy script on each images found in the input directory, or using tifffile in Python.

Specify the path to a directory with .ome.tiff files, then the script will create a "pyramidal" subfolder with your pyramidalized images in it.

Install

Install conda

If not installed already, install Miniforge, as user, add to PATH and make it the default interpreter. For more information, you can check this page. Open a terminal, run conda init and restart the terminal.

Create a virtual environment (that can be the same than the one for cuisto if you plan to use that later on) :

conda create -n cuisto-env python=3.12

Install pyramid-creator

Within a virtual environment with Python 3.12, install with pip from the terminal :

pip install pyramid-creator

To enable the Python backend, ask for the required dependencies instead :

pip install pyramid-creator[python_backend]

To use the QuPath backend, a working QuPath installation is required, and the pyramid-creator command needs to be aware of its location.

To do so, first, install QuPath. By default, it will install in ~\AppData\QuPath-0.X.Y. In any case, note down the installation location.

Then, you have several options :

• Create a file in your user directory called "QUPATH_PATH" (without extension), containing the full path to the QuPath console executable. In my case, it reads : C:\Users\glegoc\AppData\Local\QuPath-0.5.1\QuPath-0.5.1 (console).exe. Then, the pyramid-creator script will read this file to find the QuPath executable.
• Specify the QuPath path as an option when calling the command line interface (see the Usage section) :

pyramid-creator /path/to/your/images --qupath-path "C:\Users\glegoc\AppData\Local\QuPath-0.5.1\QuPath-0.5.1 (console).exe"

• Specify the QuPath path as an option when using the package in a Python script (see the Usage section) :

from pyramid_creator import pyramidalize_directory
pyramidalize_directory("/path/to/your/images/", qupath_path="C:\Users\glegoc\AppData\Local\QuPath-0.5.1\QuPath-0.5.1 (console).exe")

• If you're using Windows, using QuPath v0.6.0, v0.5.1 or v0.5.0 and chose the default installation location, pyramid-creator should find it automatically and write it down in the "QUPATH_PATH" file by itself.

Usage

As a command line interface (CLI)

From a terminal within the virtual environment in which you installed videocutter, you can check the default values with :

pyramid-creator --help

Then, here are some examples of usage :

• Pyramidalize all .ome.tiff files found in a directory, using default values (therefore using QuPath backend)

pyramid-creator /path/to/your/images

• Change the tile size

pyramid-creator /path/to/your/images --tile-size 1024

• Specify the path to a custom groovy script. The latter should take exactly the same number of arguments as pyramid-creator/scripts/createPyramids.groovy

pyramid-creator /path/to/your/images --script-path /path/to/your/custom/script.groovy

• Use the Python backend instead of QuPath :

pyramid-creator /path/to/your/images --no-use-qupath

From a Python script

Copy the example from examples/create_pyramids.py, fill in the parameters and run the script.

Credits

pyramid-creator is basically a wrapper around QuPath or tifffile for the Python backend.