cellularization-dynamics 0.2.5

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

Quick install with conda (three steps)

Use a dedicated conda environment so dependencies stay isolated. The examples below name it **cdynamics**; you can pick any name.

1. Create a new environment (Python 3.10 or newer is required):

conda create -n cdynamics python=3.12 -y

2. Activate it:

conda activate cdynamics

3. Install from PyPI:

pip install cellularization-dynamics

That installs the **cellularization_dynamics** package and registers the **cdynamics** command on this environment’s PATH. Continue to Start below.

Start

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

cdynamics

How to use?

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).