cellularization-dynamics 0.2.0

Desktop GUI for cellularization annotation and output generation

Cellularization Dynamics

Desktop app for cellularization annotation and output generation. The repository is GUI-first: run the GUI via cdynamics or python -m cellularization_dynamics; batch/Snakemake workflows are not used.

Install

pip (recommended for end users)

With your conda environment activated:

pip install /path/to/CellularizationDynamics

Or from a clone of this repository (editable install while developing):

pip install -e .

This installs the cellularization_dynamics package (with nested app and core modules) and registers the cdynamics command on your environment’s PATH.

conda (optional)

If you use environment.yaml from the repository root:

conda env create -f environment.yaml
conda activate celludynamics-gui

Start

After a pip install, from any working directory (with the same environment active):

cdynamics

From a source checkout, after pip install -e . (so the package is importable), or from any directory once the package is installed:

python -m cellularization_dynamics

or:

python -m cellularization_dynamics.app

Imports use the cellularization_dynamics top-level name, so they do not collide with unrelated PyPI packages named app or core.

Layout

• cellularization_dynamics/app/ — PyQt6 application.
• cellularization_dynamics/core/ — shared image/geometry code (kymograph, straightening, spline, exports).

Config and state

Each sample work directory has a single config.yaml with schema_version: 2. It holds acquisition settings (acquisition.source_movie points at the original TIFF; no duplicate trimmed stack), kymograph timing, spline options, apical alignment, straightening metadata, spline-fit metadata, and derived summaries. Legacy layouts with separate track/*.yaml files are merged into this file on first load.

GUI workflow

1. Add one or more .tif movies (drag-and-drop or Open Files).
2. Select a movie from the list.
3. Set acquisition parameters (px2micron, movie_time_interval_sec; optional smoothing, degree) — extracted from movie metadata when available (e.g. ImageJ-saved TIFFs).
4. Analyze — records the source movie path in config.yaml and writes track/Kymograph.tif next to the movie.
5. Adjust the cytoplasm threshold and island (apical) mode as needed; place at least two points on the cellularization front in the straightened view.
6. Save — writes mask, alignment metadata, and front annotation under the work folder.
7. Generate Outputs — straightens the kymograph, fits the spline, exports output.csv (main tabular result in the sample folder), and renders figure/video products (e.g. Cellularization.png, Cellularization_front_markers.mp4).

Outputs are written next to each input movie in a folder CDynamics-<movie filename> (see app/services/output_layout.py).