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A plugin to visualize and convert Snouty data.

Project description


License MIT PyPI Python Version tests codecov napari hub


Easy to use plugin for opening raw Snouty files and converting them to native view.


Intended Audience & Supported Data

This plugin is intended for those using a SOLS (Snouty) microscope collected via Alfred Millett-Sikking's code.

This plugin accepts a folder with at least subdirectories of data and metadata as an input.


A. Getting the plugin working (choose either a or b, you don't have to do both)

a. Through pip-install:

  1. pip install snouty-viewer (within a virtual environment of Python 3.8, 3.9, or 3.10 recommended)
  2. Open up napari

b. Through Napari:

  1. Open up napari
  2. Plugins > Install/Uninstall plugins
  3. Search for "snouty-viewer"
  4. Install
  5. (Maybe need to) reopen napari

B. Viewing raw Snouty data

  • Drag and drop a root folder of your Snouty data. This is the folder that includes the data and metadata subfolders.
  • Select "Snouty Viewer" for opening.

C. Converting raw Snouty data to its native view

  1. Click plugins, snouty-viewer: Native View
  2. Select the file you want to convert
  3. Press Run

D. Saving your native view file

  1. Select the file you want to save
  2. File > Save Selected Layer(s)...
  3. Select where you want to save your file
  4. Write your file name (recommended to end in .tif)
  5. Save
  6. Wait (this could take a few minutes depending on your file's size)

Getting Help

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.


You can install snouty-viewer via pip:

pip install snouty-viewer

To install latest development version :

pip install git+


Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.


Distributed under the terms of the MIT license, "snouty-viewer" is free and open source software


If you encounter any problems, please file an issue along with a detailed description.

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