Data, Protocols & Code

Code

WHOLISTIC registration code

GitHub URL: View Code

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

WHOLISTIC segmentation code

GitHub URL: View Code

Volumetric segmentation code used to segment WHOLISTIC datasets.

WHOLISTIC spectral clustering code

GitHub URL: View Code

Spectral clustering using coherence or correlation as similarity metric.

WHOLISTIC coherence k-means

GitHub URL: View Code

Coherence k-means clustering.

Data

Anatomical stack of pancellular Danionella GCaMP8m

Data URL: Download Data

Anataomical stack of pancellular transgenic line.

Anatomical stack of pancellular Danio Rerio GCaMP7f line

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Anataomical stack of pancellular transgenic line.

ExM demo dataset - vasculo-ventricular system

Data URL: Download Data

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

Data URL: Download Data

Anataomical stack of pancellular transgenic line.

Whole Body Geometric Model

Data URL: Download Data

GitHub URL: View Code

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

Lines

Transgenic lines

File URL: View Files

Protocols

Expansion Microscopy Protocol

Protocol URL: View Protocol

Complete protocol for expansion microscopy on zebrafish, including sample preparation, expansion, and imaging procedures.