pycat-napari

What it is and what it does

PyCAT-Napari is a low/no-code desktop application for analyzing biomolecular condensates in microscopy images. Built on napari, it provides a graphical interface to segment condensates, measure their properties (area, intensity, shape, texture), perform colocalization analysis, track trajectories over time, and estimate biophysical parameters like saturation concentration and diffusion rates. It handles 2D single images, Z-stacks, and time-series acquisitions in both fluorescence and brightfield modalities.

The package bundles 28 runtime dependencies—including numpy, scipy, scikit-image, torch, cellpose, and PyQt5—to deliver image processing, machine-learning-based segmentation, statistical analysis, and a full GUI. It is designed for researchers without programming experience, offering batch processing via JSON configuration and specialized pipelines for cellular condensates, in-vitro droplets, time-series analysis, and fibril structures. Optional GPU acceleration is available for Cellpose segmentation and morphological operations.

Use it for:

• Segment and measure fluorescent biomolecular condensates in fixed or live-cell images without writing code.
• Analyze colocalization between two or more fluorescent channels using object-based and pixel-wise metrics.
• Track condensate trajectories over time and measure fusion kinetics, diffusion, and coarsening mechanisms.
• Estimate saturation concentration (C_sat) from intensity distributions and dilution-series experiments.
• Process large time-series or Z-stack acquisitions in batch mode by recording GUI actions and replaying them across a folder.
• Measure morphological complexity (fractal dimension, lacunarity) and spatial organization (DBSCAN clustering, Voronoi) of condensate ensembles.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

PyCAT-Napari is a napari-based desktop application for detecting, measuring, and analyzing biomolecular condensates in fluorescence and brightfield microscopy images, with support for 2D, Z-stack, and time-series data.

Yes, if you are a biologist or microscopist analyzing condensates and want a low-code GUI tool. The package is actively maintained, permissively licensed, has no known vulnerabilities, and offers a comprehensive feature set tailored to condensate research. Install friction is low for a pure-Python package, though the 28 dependencies mean a dedicated environment is prudent. Not suitable if you need Python 3.11 or earlier, or if you prefer a command-line or programmatic API over a GUI.

Install

pycat-napari on PyPI

pip install pycat-napari

uv add pycat-napari

poetry add pycat-napari

Installing pycat-napari

Before you install

Low friction: pure Python wheel with no compiled dependencies beyond its runtime stack. Active maintenance with a release 8 days ago. However, 28 runtime dependencies including torch, cellpose, and PyQt5 mean installation time and disk footprint are substantial; plan for a dedicated environment.

License in practice

BSD 3-Clause permissive license. You may use, modify, and distribute the software freely provided you retain copyright notices and disclaimers. No restrictions on commercial use.

Quickstart

pip install pycat-napari
python -c "from pycat_napari import __version__; print(__version__)"
# Then launch the GUI: pycat-napari (or equivalent entry point)

Requires Python 3.12.x exactly; Python 3.13 and newer are not supported. Earlier versions (3.9, 3.11) are no longer supported as of v1.5.39.

Verify before relying

• Whether the entry point command 'pycat-napari' is automatically created on install or requires manual setup.
• Whether GPU acceleration via CuPy is automatically detected and enabled, or requires explicit configuration.
• Whether the optional TrackMate integration (headless Fiji, ~500MB–1GB) is downloaded on first use or requires manual installation.
• Performance and memory requirements for typical time-series or Z-stack workflows beyond the stated 8GB minimum.

Package facts

Evidence: pycat_napari-1.6.458-py3-none-any.whl

Keywords: bio-image, condensate, fluorescence, image analysis, microscopy, napari, pycat, scientific

Tags

More Visualization packages