fucciphase 0.0.1__tar.gz → 0.0.2__tar.gz

{fucciphase-0.0.1 → fucciphase-0.0.2}/.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.13.3
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -22,7 +22,7 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.18.2
     hooks:
       - id: mypy
         files: "^src/"

{fucciphase-0.0.1 → fucciphase-0.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fucciphase
-Version: 0.0.1
+Version: 0.0.2
 Summary: Cell cycle analysis plugin.
 Project-URL: homepage, https://github.com/nobias-ht/fucciphase
 Project-URL: repository, https://github.com/nobias-ht/fucciphase
@@ -57,7 +57,7 @@ Obtain cell cycle information from FUCCI fluorescence intensities.
 The best way to run fucciphase is to install it in a virtual conda environment.
 Make sure that git is installed and can be called from the command line.
 
-(SOON) To install from pip:
+To install from pip:
 
 ```bash
 pip install fucciphase

{fucciphase-0.0.1 → fucciphase-0.0.2}/README.md

@@ -15,7 +15,7 @@ Obtain cell cycle information from FUCCI fluorescence intensities.
 The best way to run fucciphase is to install it in a virtual conda environment.
 Make sure that git is installed and can be called from the command line.
 
-(SOON) To install from pip:
+To install from pip:
 
 ```bash
 pip install fucciphase

fucciphase-0.0.2/example/reproducibility/PaperVideo/README.md

@@ -0,0 +1,25 @@
+Process a TrackMate file through the command-line interface (CLI):
+
+```
+fucciphase merged_linked.ome.xml -ref ../../example_data/hacat_fucciphase_reference.csv -dt 0.25 -m MEAN_INTENSITY_CH1 -c MEAN_INTENSITY_CH2 --generate_unique_tracks true
+```
+
+To get more info, run
+```
+fucciphase -h
+```
+
+Visualize the file from the CLI:
+
+We provide a downscaled version of the video for faster processing:
+
+```
+fucciphase-napari merged_linked.ome.xml_processed.csv downscaled_hacat.ome.tif -m 0 -c 1 -s 2 --pixel_size 0.544
+```
+
+Please adjust segmentation contours etc. in napari.
+Consider [napari-animate](https://napari.org/napari-animation/) to prepare animations.
+
+Click on the thumbnail for an example:
+[![Preview of the video](https://raw.githubusercontent.com/Synthetic-Physiology-Lab/fucciphase/cli/example/reproducibility/PaperVideo/thumbnail.png)](https://raw.githubusercontent.com/Synthetic-Physiology-Lab/fucciphase/cli/example/reproducibility/PaperVideo/video_downscaled_hacat.mp4)
+