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.
Release files for napari-spotiflow 0.4.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| napari_spotiflow-0.4.5.tar.gz | 232.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| napari_spotiflow-0.4.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 250.2 kB
Release files / napari_spotiflow-0.4.5.tar.gz
| Download URL | napari_spotiflow-0.4.5.tar.gz |
|---|---|
| Size | 232.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.14.5
|
Release files / napari_spotiflow-0.4.5-py3-none-any.whl
| Download URL | napari_spotiflow-0.4.5-py3-none-any.whl |
|---|---|
| Size | 18.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.14.5
|
