napari-spotiflow

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.

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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