pykrait 0.3.2__tar.gz → 0.4.0__tar.gz

pykrait-0.4.0/.gitignore

@@ -0,0 +1,63 @@
+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+.Python
+
+# Distribution / packaging
+dist/
+build/
+*.egg-info/
+*.egg
+MANIFEST
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# uv
+.uv/
+uv.lock
+
+# Testing
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+
+# Linting
+.ruff_cache/
+.mypy_cache/
+
+# Jupyter
+.ipynb_checkpoints/
+
+# Docs
+docs/_build/
+docs/autoapi/
+docs/source/_autosummary/
+docs/make.bat
+docs/Makefile
+
+# IDEs
+.vscode/
+.idea/
+.claude/
+*.swp
+*.swo
+
+# macOS
+.DS_Store
+
+# Secrets
+.env
+*.pem
+
+# cellpose models
+cellpose_models/
+notebooks/batch_notebook.ipynb
+
+# local notebooks, may contain real data paths and executed outputs
+notebooks/local_*.ipynb

{pykrait-0.3.2 → pykrait-0.4.0}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2025 Phaleanopsis
+Copyright (c) 2026 Phaleanopsis
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

pykrait-0.4.0/PKG-INFO

@@ -0,0 +1,178 @@
+Metadata-Version: 2.5
+Name: pykrait
+Version: 0.4.0
+Summary: Python Calcium Recording Analysis and Interpretation Toolbox
+Author-email: phaleanopsis <22663502+phaleanopsis@users.noreply.github.com>
+License: MIT
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Requires-Dist: aicspylibczi>=3.3.1
+Requires-Dist: bioio-czi<5,>=2.4.0
+Requires-Dist: bioio-imageio<2
+Requires-Dist: bioio-ome-tiff<2,>=1.1.0
+Requires-Dist: bioio-tifffile<2,>=1.3.0
+Requires-Dist: bioio<4,>=3.2.0
+Requires-Dist: cellpose<5,>=4.0.8
+Requires-Dist: dask>=2025.5.1
+Requires-Dist: fsspec>=2022.8.0
+Requires-Dist: imagecodecs>=2025.3.30
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: numcodecs<0.16,>=0.15
+Requires-Dist: numpy>2
+Requires-Dist: opencv-python-headless>=4.10.0.84
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: psutil>=6.0
+Requires-Dist: pylibczirw>=6.0; sys_platform != 'darwin' or platform_machine != 'x86_64'
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: scikit-image>=0.25.2
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: tifffile>=2025.5.10
+Requires-Dist: tqdm>=4.66
+Requires-Dist: xarray>=2025.12
+Requires-Dist: zarr>=2.15.0
+Requires-Dist: zstandard>=0.23.0
+Provides-Extra: dev
+Requires-Dist: build>=1.2.2.post1; extra == 'dev'
+Requires-Dist: hatch>=1.14.1; extra == 'dev'
+Requires-Dist: ipywidgets>=8.1.7; extra == 'dev'
+Requires-Dist: myst-parser>=5.0.0; extra == 'dev'
+Requires-Dist: pydata-sphinx-theme>=0.16.1; extra == 'dev'
+Requires-Dist: pytest-cov>=6.0; extra == 'dev'
+Requires-Dist: pytest>=8.4.1; extra == 'dev'
+Requires-Dist: ruff>=0.11.13; extra == 'dev'
+Requires-Dist: sphinx-autoapi>=3.6.0; extra == 'dev'
+Requires-Dist: sphinx-favicon>=1.0.1; extra == 'dev'
+Requires-Dist: sphinx>=8.1.3; extra == 'dev'
+Requires-Dist: tomli>=2.2.1; extra == 'dev'
+Requires-Dist: twine>=6.1.0; extra == 'dev'
+Provides-Extra: gui
+Requires-Dist: pyside6>=6.9.1; extra == 'gui'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Winklerlab-HD/pykrait/main/docs/_static/logo.png" alt="pyKrait" width="200">
+</p>
+
+<h1 style="text-align: center;">pyKrait</h1>
+
+<p align="center">
+  <a href="https://pypi.org/project/pykrait/"><img src="https://img.shields.io/pypi/v/pykrait" alt="PyPI"></a>
+  <a href="https://pypi.org/project/pykrait/"><img src="https://img.shields.io/pypi/pyversions/pykrait" alt="Python versions"></a>
+  <a href="https://github.com/Winklerlab-HD/pykrait/actions"><img src="https://img.shields.io/github/actions/workflow/status/Winklerlab-HD/pykrait/CI.yaml" alt="CI"></a>
+    <a href="https://pykrait.readthedocs.io"><img src="https://img.shields.io/readthedocs/pykrait" alt="Docs"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-green" alt="License"></a>
+</p>
+<p align="center">
+  End-to-end pipeline for segmenting cells, detecting calcium peaks,<br>
+  and quantifying oscillation periodicity and spatial synchronicity<br>
+  from time-lapse microscopy.
+</p>
+
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Winklerlab-HD/pykrait/main/docs/_static/pyKrait_steps.png" alt="Analysis Steps of the pykrait package" width="600">
+</p>
+
+## Overview
+pyKrait (**py**thon **C**alcium **r**ecording **a**nalysis and **i**nterpretation **t**oolbox) automatically processes calcium-imaging videos (.czi, .tif, .tiff) and computes calcium activity, peak statistics, periodicity scores, and neighbour-aware synchronicity z-scores.
+
+## Installation
+
+It is recommended to install pyKrait in a virtual environment using either venv or uv. The graphical user interface is optional, install it with `pip install "pykrait[gui]"`. 
+
+### Using `uv`
+
+```bash
+uv venv --python 3.12
+source .venv/bin/activate           # Windows: .venv\Scripts\activate
+uv pip install 'pykrait[gui]'
+```
+
+### Standard `venv`
+
+```bash
+python -m venv .venv
+source .venv/bin/activate           # Windows: .venv\Scripts\activate
+pip install --upgrade pip
+pip install "pykrait[gui]"
+```
+
+
+## Quickstart
+
+### Launch the GUI
+
+From inside the activated virtual environment:
+```bash
+python -m pykrait
+```
+or
+```bash
+uv run python -m pykrait
+```
+The GUI then walks you through video selection, segmentation, peak detection, periodicity, and synchronicity, and lets you save results to disk.
+
+### Batch process an entire folder
+
+```python
+from pykrait.pipeline.pipeline import BatchExperiment, AnalysisParameters
+from pykrait.io.files import concat_analysis_files
+
+experiment = BatchExperiment(
+    folder="/path/to/videos",
+    params=AnalysisParameters(),
+    extension=".czi",
+)
+experiment.run()
+
+concat_analysis_files("/path/to/videos", filetype="output")
+```
+
+This produces one `Analysis_<video>/` directory per video and an `analysis_output_overview.csv` at the root of the folder.
+
+To analyze videos in subfolders, pass `recursive=True`; to analyze only some of the acquisitions, pass `filter_string` / `exclude_string` (e.g. `filter_string="*_timeseries.czi"`, where a pattern with `*`, `?` or `[]` matches the whole file name and anything else matches as a substring).
+
+## Example Notebooks
+
+| Scenario | Notebook |
+|----------|----------|
+| Run a folder with custom parameters | [notebooks/example_batch_with_custom_parameters](https://github.com/Winklerlab-HD/pykrait/blob/main/notebooks/example_batch_with_custom_parameters.ipynb) |
+| Re-run a folder reusing saved parameters and cached masks | [notebooks/example_batch_reusing_parameters](https://github.com/Winklerlab-HD/pykrait/blob/main/notebooks/example_batch_reusing_parameters.ipynb) |
+| Inspect or refine a single video interactively | Launch the GUI: `python -m pykrait` |
+
+## How it works
+
+For each video, pyKrait runs the following stages:
+
+1. **Load** — lazy `Dask` array via `bioio` (`.czi`, `.tif`, `.tiff`).
+2. **Correct motion** *(optional, off by default)* — align every frame to a template, either by a rigid translation or by a mesh-based / polynomial optical-flow warp.
+3. **Project** — STD or SUM projection across time, with optional CLAHE.
+4. **Segment** — Cellpose (`cpsam` by default, or a custom model path).
+5. **Extract** — per-cell mean intensity per frame, computed lazily on Dask.
+6. **Detrend** — Blackman-windowed sinc filter (cf. pyBOAT).
+7. **Detect peaks** — `scipy.signal.find_peaks` with width / height / prominence thresholds.
+8. **Periodicity** — STD and CoV of inter-peak intervals, scored against a shuffled-peaks null.
+9. **Adjacency** — neighbour graph from segmented masks (kernel-based proximity).
+10. **Synchronicity** — co-firing peaks within a time window and topological distance, z-scored against label-shuffled controls.
+
+## Documentation
+
+Full API reference and tutorials: **<https://pykrait.readthedocs.io/en/latest/>**.
+
+## Citation
+
+If you use pyKrait, please cite the [preprint](https://www.biorxiv.org/content/10.64898/2026.05.10.723715v1): Hebach, N. R., Olshausen, N., Schlag, J., Mayer, C. D., Henkenjohann, J., Kraft, T., Bang, S., Thommek, C., Nürnberg, C., Horsak, N. E., Hoffmann, D. C., Kourtesakis, A., Porzberg, N., Flores Valle, A., Linke, C. Z., Yang, Y., Azorín, D. D., Hausmann, D., Venkataramani, V., … Karreman, M. A. (2026). Collective cancer cell calcium activity drives brain metastasis. bioRxiv, 2026.05.10.723715. https://doi.org/10.64898/2026.05.10.723715
+
+## Acknowledgements
+
+pyKrait builds on and heavily uses prior open-source work:
+
+- [Cellpose](https://github.com/MouseLand/cellpose) for cell segmentation
+- [pyBOAT](https://github.com/tensionhead/pyBOAT) for the sinc-filter detrending approach
+- [bioio](https://github.com/bioio-devs/bioio) for image I/O
+- [Dask](https://www.dask.org/) for lazy array computation
+

pykrait-0.4.0/README.md

@@ -0,0 +1,123 @@
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Winklerlab-HD/pykrait/main/docs/_static/logo.png" alt="pyKrait" width="200">
+</p>
+
+<h1 style="text-align: center;">pyKrait</h1>
+
+<p align="center">
+  <a href="https://pypi.org/project/pykrait/"><img src="https://img.shields.io/pypi/v/pykrait" alt="PyPI"></a>
+  <a href="https://pypi.org/project/pykrait/"><img src="https://img.shields.io/pypi/pyversions/pykrait" alt="Python versions"></a>
+  <a href="https://github.com/Winklerlab-HD/pykrait/actions"><img src="https://img.shields.io/github/actions/workflow/status/Winklerlab-HD/pykrait/CI.yaml" alt="CI"></a>
+    <a href="https://pykrait.readthedocs.io"><img src="https://img.shields.io/readthedocs/pykrait" alt="Docs"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-green" alt="License"></a>
+</p>
+<p align="center">
+  End-to-end pipeline for segmenting cells, detecting calcium peaks,<br>
+  and quantifying oscillation periodicity and spatial synchronicity<br>
+  from time-lapse microscopy.
+</p>
+
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Winklerlab-HD/pykrait/main/docs/_static/pyKrait_steps.png" alt="Analysis Steps of the pykrait package" width="600">
+</p>
+
+## Overview
+pyKrait (**py**thon **C**alcium **r**ecording **a**nalysis and **i**nterpretation **t**oolbox) automatically processes calcium-imaging videos (.czi, .tif, .tiff) and computes calcium activity, peak statistics, periodicity scores, and neighbour-aware synchronicity z-scores.
+
+## Installation
+
+It is recommended to install pyKrait in a virtual environment using either venv or uv. The graphical user interface is optional, install it with `pip install "pykrait[gui]"`. 
+
+### Using `uv`
+
+```bash
+uv venv --python 3.12
+source .venv/bin/activate           # Windows: .venv\Scripts\activate
+uv pip install 'pykrait[gui]'
+```
+
+### Standard `venv`
+
+```bash
+python -m venv .venv
+source .venv/bin/activate           # Windows: .venv\Scripts\activate
+pip install --upgrade pip
+pip install "pykrait[gui]"
+```
+
+
+## Quickstart
+
+### Launch the GUI
+
+From inside the activated virtual environment:
+```bash
+python -m pykrait
+```
+or
+```bash
+uv run python -m pykrait
+```
+The GUI then walks you through video selection, segmentation, peak detection, periodicity, and synchronicity, and lets you save results to disk.
+
+### Batch process an entire folder
+
+```python
+from pykrait.pipeline.pipeline import BatchExperiment, AnalysisParameters
+from pykrait.io.files import concat_analysis_files
+
+experiment = BatchExperiment(
+    folder="/path/to/videos",
+    params=AnalysisParameters(),
+    extension=".czi",
+)
+experiment.run()
+
+concat_analysis_files("/path/to/videos", filetype="output")
+```
+
+This produces one `Analysis_<video>/` directory per video and an `analysis_output_overview.csv` at the root of the folder.
+
+To analyze videos in subfolders, pass `recursive=True`; to analyze only some of the acquisitions, pass `filter_string` / `exclude_string` (e.g. `filter_string="*_timeseries.czi"`, where a pattern with `*`, `?` or `[]` matches the whole file name and anything else matches as a substring).
+
+## Example Notebooks
+
+| Scenario | Notebook |
+|----------|----------|
+| Run a folder with custom parameters | [notebooks/example_batch_with_custom_parameters](https://github.com/Winklerlab-HD/pykrait/blob/main/notebooks/example_batch_with_custom_parameters.ipynb) |
+| Re-run a folder reusing saved parameters and cached masks | [notebooks/example_batch_reusing_parameters](https://github.com/Winklerlab-HD/pykrait/blob/main/notebooks/example_batch_reusing_parameters.ipynb) |
+| Inspect or refine a single video interactively | Launch the GUI: `python -m pykrait` |
+
+## How it works
+
+For each video, pyKrait runs the following stages:
+
+1. **Load** — lazy `Dask` array via `bioio` (`.czi`, `.tif`, `.tiff`).
+2. **Correct motion** *(optional, off by default)* — align every frame to a template, either by a rigid translation or by a mesh-based / polynomial optical-flow warp.
+3. **Project** — STD or SUM projection across time, with optional CLAHE.
+4. **Segment** — Cellpose (`cpsam` by default, or a custom model path).
+5. **Extract** — per-cell mean intensity per frame, computed lazily on Dask.
+6. **Detrend** — Blackman-windowed sinc filter (cf. pyBOAT).
+7. **Detect peaks** — `scipy.signal.find_peaks` with width / height / prominence thresholds.
+8. **Periodicity** — STD and CoV of inter-peak intervals, scored against a shuffled-peaks null.
+9. **Adjacency** — neighbour graph from segmented masks (kernel-based proximity).
+10. **Synchronicity** — co-firing peaks within a time window and topological distance, z-scored against label-shuffled controls.
+
+## Documentation
+
+Full API reference and tutorials: **<https://pykrait.readthedocs.io/en/latest/>**.
+
+## Citation
+
+If you use pyKrait, please cite the [preprint](https://www.biorxiv.org/content/10.64898/2026.05.10.723715v1): Hebach, N. R., Olshausen, N., Schlag, J., Mayer, C. D., Henkenjohann, J., Kraft, T., Bang, S., Thommek, C., Nürnberg, C., Horsak, N. E., Hoffmann, D. C., Kourtesakis, A., Porzberg, N., Flores Valle, A., Linke, C. Z., Yang, Y., Azorín, D. D., Hausmann, D., Venkataramani, V., … Karreman, M. A. (2026). Collective cancer cell calcium activity drives brain metastasis. bioRxiv, 2026.05.10.723715. https://doi.org/10.64898/2026.05.10.723715
+
+## Acknowledgements
+
+pyKrait builds on and heavily uses prior open-source work:
+
+- [Cellpose](https://github.com/MouseLand/cellpose) for cell segmentation
+- [pyBOAT](https://github.com/tensionhead/pyBOAT) for the sinc-filter detrending approach
+- [bioio](https://github.com/bioio-devs/bioio) for image I/O
+- [Dask](https://www.dask.org/) for lazy array computation
+

{pykrait-0.3.2 → pykrait-0.4.0}/pyproject.toml

@@ -1,42 +1,51 @@
 [project]
 name = "pykrait"
-version = "0.3.2"
-description = "Python Calcium Recording Analysis and Inference Toolbox"
+version = "0.4.0"
+description = "Python Calcium Recording Analysis and Interpretation Toolbox"
 readme = { file = "README.md", content-type = "text/markdown" }
 license = { text = "MIT" }
 authors = [
     { name = "phaleanopsis", email = "22663502+phaleanopsis@users.noreply.github.com" }
 ]
 requires-python = ">=3.11"
+# bioio plugins and cellpose change their APIs between major versions (bioio-czi 4 removed
+# use_aicspylibczi), so they are capped at the next untested major version
 dependencies = [
     "aicspylibczi>=3.3.1",
-    "bioio>=3.0.0",
-    "bioio-czi>=2.4.0",
-    "bioio-ome-tiff>=1.1.0",
-    "bioio-tifffile>=1.3.0",
-    "bioio-imageio",
-    "cellpose>=4.0.5",
+    "bioio>=3.2.0,<4",
+    "bioio-czi>=2.4.0,<5",
+    "bioio-ome-tiff>=1.1.0,<2",
+    "bioio-tifffile>=1.3.0,<2",
+    "bioio-imageio<2",
+    "cellpose>=4.0.8,<5",
     "dask>=2025.5.1",
     "fsspec>=2022.8.0",
     "imagecodecs>=2025.3.30",
-    "lxml>=5.4.0",
     "matplotlib>=3.10.3",
-    "numcodecs<0.16",
+    # zarr 2 imports numcodecs.blosc.cbuffer_sizes, which numcodecs 0.16 removed
+    "numcodecs>=0.15,<0.16",
     "numpy>2",
-    "ome-types>=0.5.3",
-    "ome-zarr>=0.10.2",
-    "pip>=25.1.1",
-    "pydantic<2",
+    "opencv-python-headless>=4.10.0.84",
     "pyyaml>=6.0.2",
-    "resource-backed-dask-array>=0.1.0",
     "scikit-image>=0.25.2",
     "scipy>=1.15.3",
-    "xarray>2025",
+    "tifffile>=2025.5.10",
+    "tqdm>=4.66",
+    "xarray>=2025.12",
     "pandas>=2.3.1",
+    "psutil>=6.0",
+    # reads CZI files much faster than bioio; there is no wheel for Intel Macs, which
+    # fall back to bioio
+    "pylibCZIrw>=6.0; sys_platform != 'darwin' or platform_machine != 'x86_64'",
     "zstandard>=0.23.0",
-    "scikit-learn>=1.7.2",
+    "zarr>=2.15.0",
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
-
 [project.optional-dependencies]
 gui = [
     "pyside6>=6.9.1",
@@ -53,7 +62,8 @@ dev = [
     "tomli>=2.2.1",
     "twine>=6.1.0",
     "pytest>=8.4.1",
-    "pytest-cov"
+    "pytest-cov>=6.0",
+    "myst-parser>=5.0.0",
 ]
 
 [build-system]
@@ -92,17 +102,7 @@ source = ["pykrait"]
 show_missing = true
 skip_covered = true
 
-[tool.setuptools.package-data]
-"pykrait.gui.resources" = ["logo.png"]
-
 [tool.ruff]
 src = ["src"]
 line-length = 88
 target-version = "py311"
-
-[dependency-groups]
-dev = [
-    "build>=1.2.2.post1",
-    "hatch>=1.14.1",
-    "twine>=6.1.0",
-]

pykrait-0.4.0/src/pykrait/__init__.py

@@ -0,0 +1,27 @@
+import logging
+import sys
+
+
+class _StdoutHandler(logging.StreamHandler):
+    """Writes to the current sys.stdout, which notebooks and tests replace after import."""
+
+    @property
+    def stream(self):
+        return sys.stdout
+
+    @stream.setter
+    def stream(self, value):
+        pass
+
+
+# pykrait reports its progress through the "pykrait" logger. By default the messages are
+# printed to stdout as before; silence them with
+# logging.getLogger("pykrait").setLevel(logging.WARNING), or remove this handler to
+# route them through your own logging configuration.
+_logger = logging.getLogger(__name__)
+_handler = _StdoutHandler()
+_handler.setFormatter(logging.Formatter("%(message)s"))
+_logger.addHandler(_handler)
+if _logger.level == logging.NOTSET:  # keep a level that was set before the import
+    _logger.setLevel(logging.INFO)
+_logger.propagate = False

pykrait-0.4.0/src/pykrait/__main__.py

@@ -0,0 +1,20 @@
+"""
+Copyright © 2026 Phaleanopsis
+"""
+
+# src/pykrait/__main__.py
+import sys
+
+try:
+    from pykrait.gui.app import AppController
+except ImportError as e:
+    if getattr(e, "name", None) and e.name.startswith("PySide6"):
+        sys.exit(
+            "The pyKrait GUI needs the optional GUI dependencies. "
+            'Install them with: pip install "pykrait[gui]"'
+        )
+    raise
+
+if __name__ == "__main__":
+    app_controller = AppController()
+    app_controller.run()

{pykrait-0.3.2 → pykrait-0.4.0}/src/pykrait/gui/app.py

@@ -1,3 +1,4 @@
+import logging
 import sys
 import os
 import warnings
@@ -8,15 +9,18 @@ from pykrait.gui.fileselection import FileSelectionWindow
 from pykrait.gui.mainwindow import MainWindow
 from pykrait.io.files import get_pykrait_version
 
+logger = logging.getLogger(__name__)
+
+
 def warning_no_source_line(message, category, filename, lineno, file=None, line=None):
     return f"{filename}:{lineno}: {category.__name__}: {message}\n"
 
+
 class AppController:
     def __init__(self):
-
         # format warnings to not print the source line every time
         warnings.formatwarning = warning_no_source_line
-        
+
         self.app = QApplication(sys.argv)
 
         # Loading icon from resources
@@ -25,7 +29,6 @@ class AppController:
             from importlib.resources import files
 
             icon_path = files("pykrait.gui.resources").joinpath("logo.png")
-            os.path.exists(icon_path)
         except Exception:
             icon_path = os.path.abspath(
                 os.path.join(
@@ -36,28 +39,21 @@ class AppController:
                     "logo.png",
                 )
             )
-            os.path.exists(icon_path)
         if os.path.exists(icon_path):
-            appIcon.addFile(str(icon_path), QSize(16, 16))
-            appIcon.addFile(str(icon_path), QSize(24, 24))
-            appIcon.addFile(str(icon_path), QSize(32, 32))
-            appIcon.addFile(str(icon_path), QSize(48, 48))
-            appIcon.addFile(str(icon_path), QSize(64, 64))
-            appIcon.addFile(str(icon_path), QSize(256, 256))
+            for size in (16, 24, 32, 48, 64, 256):
+                appIcon.addFile(str(icon_path), QSize(size, size))
             self.app.setWindowIcon(appIcon)
         else:
-            print(f"Warning: Icon file not found at {icon_path}")
+            logger.warning(f"Warning: Icon file not found at {icon_path}")
 
         # Set application name and version
         self.app.setApplicationName("pyKrait")
         version = get_pykrait_version()
         if version is not None:
             self.app.setApplicationVersion(version)
-        self.file_selection = FileSelectionWindow()
-        self.file_selection.analysis_complete.connect(self.on_analysis_complete)
-        self.file_selection.show()
-        
-        #updating the style
+        self._open_file_selection()
+
+        # updating the style
         self.app.setStyle("Fusion")
         light_palette = self.app.style().standardPalette()
         self.app.setPalette(light_palette)
@@ -72,6 +68,7 @@ class AppController:
         # Launch main window, keep reference
         self.main_window = MainWindow(
             frames=results["frames"],
+            display_channel=results.get("intensity_channel", 0),
             mask=results["masks"],
             rois=results["rois"],
             mean_intensities=results["mean_intensities"],
@@ -81,6 +78,11 @@ class AppController:
         )
         self.main_window.show()
 
+    def _open_file_selection(self):
+        self.file_selection = FileSelectionWindow()
+        self.file_selection.analysis_complete.connect(self.on_analysis_complete)
+        self.file_selection.show()
+
     def run(self):
         sys.exit(self.app.exec())
 
@@ -89,6 +91,4 @@ class AppController:
             self.main_window.close()
             self.main_window = None
 
-        self.file_selection = FileSelectionWindow()
-        self.file_selection.analysis_complete.connect(self.on_analysis_complete)
-        self.file_selection.show()
+        self._open_file_selection()