diff --git a/README.md b/README.md index c57bfe8a32b2b49c617427302475fb925e758bc4..d194e718c2d176f6c2e8671be8c08b8d24738599 100644 --- a/README.md +++ b/README.md @@ -7,31 +7,85 @@ [](https://codecov.io/gh/aaristov/napari-segment) [](https://napari-hub.org/plugins/napari-segment) -Segment organoids and measure intensities +Segment organoids in brightfield from nd2 stack ---------------------------------- This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template. -<!-- -Don't miss the full getting started guide to set up your new package: -https://github.com/napari/cookiecutter-napari-plugin#getting-started - -and review the napari docs for plugin developers: -https://napari.org/plugins/stable/index.html ---> ## Installation -You can install `napari-segment` via [pip]: - - pip install napari-segment - - - -To install latest development version : - - pip install git+https://github.com/aaristov/napari-segment.git +```pip install git+https://github.com/aaristov/napari-segment.git``` + +## Usage for segmentation + +1. Drag your nd2 file into napari +2. Lauch Plugins -> napari-segment: Segment prognoid +3. Select the brightfield channel +4. The data is lazily loaded from nd2 dataset and dynamically segmented in the viewer. +5. Theshold and erode parameters allow you to adjust segmentation -> they all will appear in the Detections layer +6. Min/max diameter and eccentricity allow you to filter out unwanted regions -> the good regions will appear in the "selected labels" layer. +7. You can deactivate the Detection layer with a checkbox. +8. Once saticfied, simply save the selected labels layer with build-in napari saver for future use and downstream analysis. + + + +## Usage for multicale zarr preview +1. Drag and drop the folder with mutiscale zarr dataset. +2. The plugin will look for the napari attributes in the .zattr file and render the stack accordingly. See the example below for 4D dataset: +```json +{ + "multiscales": { + "multiscales": [ + { + "channel_axis": 1, + "colormap": [ + "gray", + "green", + "blue" + ], + "datasets": [ + { + "path": "0" + }, + { + "path": "1" + }, + { + "path": "2" + }, + { + "path": "3" + } + ], + "lut": [ + [ + 1000, + 30000 + ], + [ + 440, + 600 + ], + [ + 0, + 501 + ] + ], + "name": [ + "BF", + "TRITC", + "mask" + ], + "title": "BF_TRITC_aligned.zarr", + "type": "nd2", + "version": "0.1" + } + ] + } +} +``` ## Contributing