T-MIDAS

This Napari plugin allows you to perform batch image processing without a graphics processing unit (GPU). It will still be fast because computations will run in parallel on your central processing unit (CPU).

This plugin provides you with a growing collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features.

napari-tmidas is a work in progress (WIP) and an evolutionary step away from the terminal / command-line version of T-MIDAS.

Installation¶

First install Napari in a virtual environment:

mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
mamba activate napari-tmidas
python -m pip install "napari[all]"

Now you can install napari-tmidas via pip:

pip install napari-tmidas

To install the latest development version:

pip install git+https://github.com/macromeer/napari-tmidas.git

Dependencies¶

For the File converter, we need some libraries to read some microscopy formats and to write ome-zarr:

pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr

Usage¶

You can find the installed plugin here:

File converter¶

You might first want to batch convert microscopy image data. Currently, this plugin supports .nd2, .lif, .ndpi, .czi and acquifer data. After launching the file converter, you can scan a folder of your choice for microscopy image data. It will also detect series images that you can preview. Start by selecting an original image in the first column of the table. This allows you to preview or convert.

File inspector¶

1. After opening Plugins > T-MIDAS > File selector, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.

2. As a result, a table appears with the found images.

3. Next, select a processing function, set parameters if applicable and Start Batch Processing.

4. You can click on the images in the table to show them in the viewer. For example first click on one of the Original Files, and then the corresponding Processed File to see an overlay.

Note that whenever you click on an Original File or Processed File in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.

Label inspector¶

If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the Plugins > T-MIDAS > Label inspector, which automatically saves your changes to the existing label image once you click the Save Changes and Continue button (bottom right).

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 BSD-3 license, "napari-tmidas" is free and open source software

Issues¶

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

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This napari plugin was generated with copier using the napari-plugin-template.