Create pyramidal OME-TIFF#

This page will guide you to use the pyramid-creator package, in the event the CZI file does not work directly in QuPath. The script will generate pyramids from OME-TIFF files exported from ZEN.

Tip

pyramid-creator can also pyramidalize images using Python only with the --no-use-qupath option.

This Python script uses QuPath under the hood, via a companion script called createPyramids.groovy. It will find the OME-TIFF files and make QuPath run the groovy script on it, in console mode (without graphical user interface).

This script is standalone, eg. it does not rely on the cuisto package. But installing the later makes sure all dependencies are installed (namely typer and tqdm with the QuPath backend and quite a few more for the Python backend).

pyramid-creator moved to a standalone package that you can find here with installation and usage instructions.

Installation#

You will find instructions on the dedicated project page over at Github.

For reference :

You will need conda, follow those instructions to install it.

Then, create a virtual environment if you didn't already (pyramid-creator can be installed in the environment for cuisto) and install the pyramid-creator package.

conda create -c conda-forge -n cuisto-env python=3.12  # not required if you already create an environment
conda activate cuisto-env
pip install pyramid-creator

To use the Python backend (with tifffile), replace the last line with :

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.

Export CZI to OME-TIFF#

OME-TIFF is a specification of the TIFF image format. It specifies how the metadata should be written to the file to be interoperable between softwares. ZEN can export to OME-TIFF so you don't need to pay attention to metadata. Therefore, you won't need to specify pixel size and channels names and colors as it will be read directly from the OME-TIFF files.

Open your CZI file in ZEN.
Open the "Processing tab" on the left panel.
Under method, choose Export/Import > OME TIFF-Export.
In Parameters, make sure to tick the "Show all" tiny box on the right.
The following parameters should be used (checked), the other should be unchecked :
- Use Tiles
- Original data "Convert to 8 Bit" should be UNCHECKED
- OME-XML Scheme : 2016-06
- Use full set of dimensions (unless you want to select slices and/or channels)
In Input, choose your file
Go back to Parameters to choose the output directory and file prefix. "_s1", "_s2"... will be appended to the prefix.
Back on the top, click the "Apply" button.

The OME-TIFF files should be ready to be pyramidalized with the create_pyramids.py script.

Usage#

See the instructions on the dedicated project page over at Github.