Protocols, Code & Data
Protocols, analysis code, datasets and transgenic lines from the WHOLISTIC project, with links to each source.
Protocols
Code
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WHOLISTIC registration code
A fast, accurate, and non-rigid image registration method for Whole-Body Cellular Activity Imaging data. -
WHOLISTIC segmentation code
Volumetric segmentation code used to segment WHOLISTIC datasets. -
WHOLISTIC spectral clustering code
Spectral clustering using coherence or correlation as similarity metric.
Data
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Anatomical stack of pancellular Danionella GCaMP8m
Anatomical stack of pancellular transgenic line. -
Anatomical stack of pancellular Danio rerio GCaMP7f line
Anatomical stack of pancellular transgenic line. -
ExM demo dataset - vasculo-ventricular system
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. -
Whole Body Geometric Model
3D geometric model of the young zebrafish built from Whole-Body Expansion Microscopy data. -
Anatomical stack of gel-embedded pancellular Danio rerio GCaMP7f line stained with DAPI and total protein stain AF488-NHS
Anatomical stack of pancellular transgenic line, gel embedded and stained for nuclei