Update create_pyramids.py, pyproject.toml, pyramid_creator.py, and 1 more file

Author: GuillaumeLeGoc

README.md

@@ -16,9 +16,9 @@ To enable the Python backend, ask for the required dependencies instead :
 pip install pyramid-creator[python_backend]
 ```
 
-To use the QuPath backend (recommended), a working QuPath installation is required, and the `pyramid-creator` command needs to be aware of its location.
+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](https://qupath.github.io). By default, it will install in AppData\QuPath-0.X.Y. In any case, note down the installation location.
+To do so, first, install [QuPath](https://qupath.github.io). 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.

examples/create_pyramids.py

@@ -7,7 +7,7 @@
 
 from pyramid_creator import pyramidalize_directory
 
-images_dir = r"E:\projects\histo\data\GN105\ZEN_EXPORT\SUB"
+images_dir = "/path/to/your/images"
 
 # --- Parameters
 # Tile size (usually 512 or 1024)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyramid-creator"
-version = "2024.12.17"
+version = "2024.12.18"
 authors = [{ name = "Guillaume Le Goc", email = "[email protected]" }]
 description = "Create pyramidal OME-TIFF from regular OME-TIFF images using QuPath or Python backend."
 readme = "README.md"
@@ -19,7 +19,7 @@ dependencies = [
 python_backend = [
   "numpy>=2",
   "scikit-image>0.22.0",
-  "tifffile>=2024.4.24"
+  "tifffile[codecs]>=2024.4.24",
 ]
 
 [project.urls]

pyramid_creator/pyramid_creator.py

@@ -17,7 +17,7 @@
 from tqdm import tqdm
 from typing_extensions import Annotated
 
-__version__ = "2024.12.17"
+__version__ = "2024.12.18"
 
 
 # --- Typer functions