snouty-viewer 0.0.4

A plugin to visualize and convert Snouty data.

snouty-viewer

Description

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.

Quickstart

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

• Open up an issue on GitHub.
• Start a thread on image.sc

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

Installation

You can install snouty-viewer via pip:

pip install snouty-viewer

To install latest development version :

pip install git+https://github.com/aelefebv/snouty-viewer.git

Contributing

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.

License

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

Issues

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