napari-file2folder

A plugin to inspect bioimages (e.g. .tif, .czi, .nd2, .lsm...) and save them as individual .tif files in a folder.

napari-file2folder is a napari plugin that is part of the Tapenade project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.

If you use this plugin for your research, please cite us.

Overview

This plugin allows you to inspect (possibly large) bioimages by displaying their shape (number of elements in each dimension), and allowing you to save each element along a chosen dimension as a separate .tif file in a folder. This is useful when you have a large movie or stack of images and you want to save each frame or slice as a separate file. Optionally, the plugin allows the user to visualize the middle element of a given dimension to help the user decide which dimension to save as separate files.

The plugin currently supports the following file formats:

• .tif
• .ome.tiff
• .zarr
• .ome.zarr
• .nd2
• .lsm
• .czi

This plugin leverages tifffile, bioio, and zarr to circumvent loading the entire images in memory, which allows inspection of very large images.

[!CAUTION] When inspecting the middle element of a dimension, or when saving one element of a dimension as a separate file, the plugin loads the element in memory, which means that at least this lone element must fit in memory.

Installation

The plugin obviously requires napari to run. If you don't have it yet, follow the instructions here.

Compatible with Python 3.9 to 3.13 (recommended: 3.12).

This plugin also provides a Napari reader, so drag-and-drop can load supported bioimages using the bioio library.

The simplest way to install napari-file2folder is via the napari plugin manager. Open Napari, go to Plugins > Install/Uninstall Packages... and search for napari-file2folder. Click on the install button and you are ready to go!

You can install napari-file2folder via pip:

pip install napari-file2folder

How to cite

If you use this plugin for your research, please cite us using the following reference:

• Jules Vanaret, Alice Gros, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili (2025) A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales. eLife 14:RP107154 ; doi:https://doi.org/10.7554/eLife.107154.2

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, "napari-file2folder" is free and open source software

Issues

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

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