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Update README.md
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uschmidt83 authored Apr 26, 2024
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Expand Up @@ -49,7 +49,7 @@ The plugin does perform input validation, i.e. it will disable the `Run` button

**Pre-trained Model**: Select a registered pre-trained model from a list. The first time a model is selected, it is downloaded and cached locally.

**Custom Model**: Provide a path to a StarDist model folder, containing at least `config.json` and a compatible neural network weights file (with suffix `.h5` or `.hdf5`). If present, `thresholds.json` is also loaded and its values can be used via the button *Set optimized postprocessing thresholds (for selected model)*.
**Custom Model**: Provide a path to a StarDist model folder, containing at least `config.json` and a compatible neural network weights file (with suffix `.h5` or `.hdf5`). If present, `thresholds.json` is also loaded and its values can be used via the button *Set optimized postprocessing thresholds (for selected model)*. If you want to use [a model from bioimage.io]([url](https://bioimage.io/#/?tags=stardist&type=model)), you first need to convert it to the regular StarDist model folder format (see how to do this [here]([url](https://nbviewer.org/github/stardist/stardist/blob/main/examples/other2D/bioimageio.ipynb#Import-bioimage.io-model-as-StarDist-model))).

**Model Axes**: A read-only text field that shows the semantic axes that the currently selected model expects as input. Additionally, we show the number of expected input channels, e.g. `YXC[2]` to indicate that the model expects a 2D input image with 2 channels. Seeing the model axes is helpful to understand whether the axes of the input image are compatible or not.

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