pyKrait

End-to-end pipeline for segmenting cells, detecting calcium peaks,
and quantifying oscillation periodicity and spatial synchronicity
from time-lapse microscopy.

Overview

pyKrait (python Calcium recording analysis and interpretation toolbox) 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]".

Standard venv

python -m venv .venv
source .venv/bin/activate           # Windows: .venv\Scripts\activate
pip install --upgrade pip
pip install pykrait

Using uv

uv venv --python 3.11
source .venv/bin/activate           # Windows: .venv\Scripts\activate
uv pip install pykrait

Quickstart

Launch the GUI

From inside the activated virtual environment:

python -m pykrait

The GUI walks you through video selection, segmentation, peak detection, periodicity, and synchronicity, and lets you save results to disk.

Batch process an entire folder

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.

Examples

How it works

For each video, pyKrait runs the following stages:

1. Load — lazy Dask array via bioio (.czi, .tif, .tiff).
2. Project — STD or SUM projection across time, with optional CLAHE.
3. Segment — Cellpose (cpsam by default, or a custom model path).
4. Extract — per-cell mean intensity per frame, computed lazily on Dask.
5. Detrend — Blackman-windowed sinc filter (cf. pyBOAT).
6. Detect peaks — scipy.signal.find_peaks with width / height / prominence thresholds.
7. Periodicity — STD and CoV of inter-peak intervals, scored against a shuffled-peaks null.
8. Adjacency — neighbour graph from segmented masks (kernel-based proximity).
9. 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/.

Acknowledgements

pyKrait builds on and heavily uses prior open-source work:

• Cellpose for cell segmentation
• pyBOAT for the sinc-filter detrending approach
• bioio for image I/O
• Dask for lazy array computation