Napari plugin for Spotiflow

License: BSD-3 PyPI Python Version tests PyPI - Downloads napari hub


Napari plugin for Spotiflow, a deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method for fluorescence microscopy. For the main repo, see here.

If you use this plugin for your research, please cite us.

  1. Open the image (or open one of our samples, e.g. File > Open Sample > napari-spotiflow > HybISS)
  2. Start the plugin Plugins > napari-spotiflow
  3. Select model (pretrained or custom trained) and optionally adjust any other parameters
  4. Click run

Supported input formats

  • 2D (YX, YXC or CYX)
  • 2D+t (TYX, TYXC or TCYX)


The plugin can be installed directly from PyPi (make sure you use a conda environment with napari and spotiflow installed):

pip install napari-spotiflow


  • 0.2.0

Last updated:

  • 09 February 2024

First released:

  • 02 February 2024


Supported data:

  • Information not submitted

Open extension:

GitHub activity:

  • Stars: 8
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:


  • spotiflow
  • npe2
  • napari