Protocols, Code & Data

Protocols

WHOLISTIC ExM: Whole-Body Expansion Microscopy with Immunofluorescence and Histological Stain

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PhotoMap: unbiased mapping of Expansion Microscopy deformation fields

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Code

WHOLISTIC registration code

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A fast, accurate, and non-rigid image registration method for Whole-Body Cellular Activity Imaging data.

WHOLISTIC segmentation code

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Volumetric segmentation code used to segment WHOLISTIC datasets.

WHOLISTIC spectral clustering code

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Spectral clustering using coherence or correlation as similarity metric.

WHOLISTIC coherence k-means

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Coherence k-means clustering.

Data

Anatomical stack of pancellular Danionella GCaMP8m

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Anatomical stack of pancellular transgenic line.

Anatomical stack of pancellular Danio Rerio GCaMP7f line

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Anatomical stack of pancellular transgenic line.

ExM demo dataset - vasculo-ventricular system

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Whole fish ExM microscopy of double transgenic sample labeling the ventricular and vascular systems. Sample: Tg(foxj1a:eGFP) x Tg(flk1:dsRED-CAAX), stained against eGFP (magenta) and dsRED (green), 10 days post-fertilization, expanded ~2×, dorsally mounted.

WHOLISTIC data

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Anataomical stack of pancellular transgenic line.

Whole Body Geometric Model

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3D geometric model of the young zebrafish built from Whole-Body Expansion Microscopy data.

Anatomical stack of gel-embedder pancellular Danio Rerio GCaMP7f line stained with DAPI and total protein stain AF488-NHS

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Anatomical stack of pancellular transgenic line, gel embedded and stained for nuclei

Lines

Transgenic lines

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