napari-spotiflow
Napari plugin for Spotiflow
Spotiflow: napari plugin
Napari plugin for Spotiflow, a deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method for 2D and 3D fluorescence microscopy images. The plugin allows using several pre-trained models as well as user-trained ones. For the main repository, 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 as well as napari.
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
Usage
- Open the image (or open one of our samples, e.g.
File > Open Sample > napari-spotiflow > HybISS) - Start the plugin
Plugins > napari-spotiflow - Select model (pre-trained or custom trained) and optionally adjust any other parameters
- Click
Detect spots
Supported input formats
- 2D (YX, YXC or CYX)
- 2D+t (TYX, TYXC or TCYX)
- 3D (ZYX, ZYXC or CZYX)
- 3D+t (TZYX, TZYXC or TCZYX)
How to cite
See the main repository's How to cite section as well as napari's citing napari section.
Version:
- 0.4.3
Last updated:
- 2025-06-16
First released:
- 2024-02-02
License:
- BSD 3-Clause
Supported data:
- Information not submitted
Plugin type:
Open extension:
Save extension:
Python versions supported:
Operating system:
- Information not submitted
Requirements:
- spotiflow
- npe2
- napari>=0.5