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3D spatial and data analysis workflow 3D spatial analysis of 3D-IF stained and optically cleared samples with UltraMicroscope Blaze™ light sheet microscope (Step 16). Post processing (stitching) in case data was acquired with tile-scanning (Step 18). Surfaces generation of autofluorescence and target region with Imaris software (Oxford Instruments) and target plane definition with “Oblique Slicer” tool (Step 20 and 20).

Journal: STAR Protocols

Article Title: Protocol for 3D-guided sectioning and deep cell phenotyping via light sheet imaging and 2D spatial multiplexing

doi: 10.1016/j.xpro.2025.104296

Figure Lengend Snippet: 3D spatial and data analysis workflow 3D spatial analysis of 3D-IF stained and optically cleared samples with UltraMicroscope Blaze™ light sheet microscope (Step 16). Post processing (stitching) in case data was acquired with tile-scanning (Step 18). Surfaces generation of autofluorescence and target region with Imaris software (Oxford Instruments) and target plane definition with “Oblique Slicer” tool (Step 20 and 20).

Article Snippet: Continue the workflow in Imaris to create orientation marks for further analysis.

Techniques: Staining, Microscopy, Software