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update documentation to depend only on specify used plugins
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zoccoler committed Aug 14, 2024
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Expand Up @@ -61,10 +61,6 @@ Alternatively, clone this repository and install the latest plugin development v

pip install git+https://github.com/zoccoler/napari-flim-phasor-plotter.git

_Optional, but we **strongly** recommend having the `devbio-napari` plugin bundle also installed for post-processing. This can be done with:_

mamba install -c conda-forge devbio-napari=0.10.0 scikit-image=0.24.0

## Usage

### Loading Raw FLIM Data
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To connect small isolated regions and remove small holes within the mask, we can use the `smooth_cluster_mask` function. This can be accessed via `Plugins -> FLIM phasor plotter -> Smooth Cluster Mask`. This will remove holes with an area smaller than the specified `fill area px` in total number of pixels and connect regions within a given `smooth radius`. Don't forget to select the layer containing the mask before running the function, because this function expects a layer with a single label (like a binary mask).

Beyond this point, we can use other plugins, like the `devbio-napari` plugin bundle, to further process the mask. For example, we can perform instance segmentation on the mask via `Tools -> Segmentation / labeling -> Connectec component labeling (scikit-image, nsbatwm)`. We can also extract features from the objects via `Tools -> Measurement tables -> Objetct Features/Properties (scikit-image, nsr)`.
Beyond this point, we can use other plugins, like the `napari-segment-blobs-and-things-with-membranes` and `napari-skimage-regionprops` plugins, to further process the mask. For example, we can perform instance segmentation on the mask via `Tools -> Segmentation / labeling -> Connectec component labeling (scikit-image, nsbatwm)`. We can also extract features from the objects via `Tools -> Measurement tables -> Objetct Features/Properties (scikit-image, nsr)`.

Below is a demonstration of the post-processing steps:

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