From 87c1eb7e6a72fc77f615de1906aa2b43fd730a24 Mon Sep 17 00:00:00 2001 From: Christina Bukas Date: Wed, 13 Apr 2022 15:00:15 +0200 Subject: [PATCH] mention napari-aicsimage --- .napari/DESCRIPTION.md | 6 ++++++ README.md | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/.napari/DESCRIPTION.md b/.napari/DESCRIPTION.md index 5459684..438ee1e 100644 --- a/.napari/DESCRIPTION.md +++ b/.napari/DESCRIPTION.md @@ -8,6 +8,12 @@ A napari plugin to automatically count lung organoids from microscopy imaging da This plugin has been developed and tested with 2D CZI microscopy images of lunch organoids. The images had been previously converted from a 3D stack to 2D using an extended focus algorithm. This plugin may be used as a baseline for developers who wish to extend the plugin to work with other types of input images and/or improve the detection algorithm. +## Dependencies + +```napari-organoid-counter``` uses the ```napari-aicsimageio```[1] plugin for reading and processing CZI images. + +[1] AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio + ## Quickstart The use of the napari-organoid-counter plugin is straightforward. After loading the image or images you wish to process into the napari viewer, you must first pre-process them by clicking the _Preprocess_ button and the image layer will automatically be updated with the result. Next, you can adjust any of the parameters used in the algorithm (downsamppling, minimum organoid diamtere and sigma, i.e. kernel sixe for the Cannny Edge Detection algorithm) by using the corresponding sliders. By clicking the _Run Organoid Counter_ button the detection algorithm will run and a new shapes layer will be added to the viewer, with bounding boxes are placed around the detected organoid. You can add, edit or remove boxes using the _layer controls_ window and update the _Number of detected organoids_ displayed by clicking the _Update Number_ button. diff --git a/README.md b/README.md index 8de24b5..bfdb741 100644 --- a/README.md +++ b/README.md @@ -47,6 +47,12 @@ the coverage at least stays the same before you submit a pull request. Distributed under the terms of the [MIT] license, "napari-organoid-counter" is free and open source software +## Dependencies + +```napari-organoid-counter``` uses the ```napari-aicsimageio```[1] plugin for reading and processing CZI images. + +[1] AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio + ## Issues If you encounter any problems, please [file an issue] along with a detailed description.