pycat-napari
Python Condensate Analysis Toolbox - A napari-based tool for biomolecular condensate analysis
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- 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.
- Low friction: pure Python wheel with no compiled dependencies beyond its runtime stack.
License · maintenance · safety
permissive license (permissive) — 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.
last release 2026-08-06 (8 days) · last repo commit 2026-08-12 · 1 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 296,990 downloads/mo, #7,892 on PyPI
Alternatives
Verify before relying
pip install pycat-napari
python -c "from pycat_napari import __version__; print(__version__)"
# Then launch the GUI: pycat-napari (or equivalent entry point)- 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.
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 on it.
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
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.
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.
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)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
| License | permissive license permissive |
| Python support | Capped below the current Python release <3.13,>=3.12 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 28 packagesavbioio-czibioio-imageiobioio-ome-tiffbioio-tifffilebioiocellposehdf5pluginimaris-ims-file-readerlargestinteriorrectanglematplotlibnaparinetworkxnumbanumpyopencv-python-headlessopenpyxlpandaspydanticpyqt5pywaveletsscikit-imagescikit-learnscipyseabornsimpleitktorchzarr |
| Maintenance | Actively maintained 8 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 296,990 / month, #7,892 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaIntended Audience :: Science/ResearchLicense :: OSI Approved :: BSD LicenseOperating System :: OS IndependentProgramming Language :: Python :: 3Programming Language :: Python :: 3.12Topic :: Scientific/Engineering :: Bio-InformaticsTopic :: Scientific/Engineering :: Image ProcessingTopic :: Scientific/Engineering :: Visualization |
Evidence: pycat_napari-1.6.458-py3-none-any.whl
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See also napari · cellpose · biotite · napari-plugin-manager · napari-console · npe2 · napari-svg · skan · napari-plugin-engine · PeakUtils