napari-spotiflow

napari-spotiflow

Napari plugin for Spotiflow

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

Logo

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.

https://github.com/weigertlab/napari-spotiflow/assets/11042162/02940480-daa9-4a21-8cf5-ad73c26c9838

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)

Installation

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

pip install napari-spotiflow

Version:

  • 0.2.0

Last updated:

  • 09 February 2024

First released:

  • 02 February 2024

License:

Supported data:

  • Information not submitted

Open extension:

GitHub activity:

  • Stars: 7
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • spotiflow
  • npe2
  • napari

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