snouty-viewer
Description
Easy to use plugin for opening raw Snouty files and converting them to native view.
Allows for saving to ome.tif files with corresponding OME-XML based metadata.
Also allows for bulk deskewing and saving directories.
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:
- pip install snouty-viewer (within a virtual environment of Python 3.8, 3.9, or 3.10 recommended)
- Open up napari
b. Through Napari:
- Open up napari
- Plugins > Install/Uninstall plugins
- Search for "snouty-viewer"
- Install
- (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
- Click plugins, snouty-viewer -> Native View
- Select the file you want to convert
- Press Deskew
D. Saving your native view file
- Select the channel (or multi-channel) layer you want to save
- File > Save Selected Layer(s)...
- Select where you want to save your file
- Title your file, ".ome.tif" will automatically be appended.
- Save with "Snouty Writer"
- Wait (this could take a few minutes depending on your file's size and your hardware)
E. Batch saving
- Click plugins, snouty-viewer -> Batch Deskew & Save
- Input a directory (without quotes) that contains 1 or more Snouty-acquired directories.
- If you want to view your deskewed outputs, check the box.
- If you want to automatically save the deskewed outputs, check the box.
- Press Deskew and save
- Wait (this could take a few minutes depending on your files' sizes and your hardware)
Getting Help
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.