Extended Data Fig. 2: Data import, export and interface of 3DCellScope. | Nature Methods

Extended Data Fig. 2: Data import, export and interface of 3DCellScope.

From: Digitalized organoids: integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology

Extended Data Fig. 2

a. Images imported into 3DCellScope for segmentation, user can run segmentation on selected image and the segmentation masks and csv files were output in results folder. b. Interface of 3DCellScope and steps to generate the results. (1) File management: Select images folder and choose image for visualization or processing. (2) Channel preprocessing: Add preprocessings for selected channels. (3) Nuclei segmentation: Select Stardist model and fit model resolution. (4) Organoid segmentation: Apply Otsu threshold or Dynamic Range threshold for organoid segmentation. (5) Cell segmentation: Run 3D watershed using intensity channel or distance map. (6) Process image: Click to start processing selected image. (7) Image/results visualization: Visualize the image and results in 2D and 3D view. (8) Data exploration: Explore data with various tools, such as generating plots, performing gating and running PCA.

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