Downloads for software published by the Burgess lab at NICHD. It's all free and you are also welcome to the source code (email: email@example.com).
The Brain Browser allows visualization and searching of 3D expression patterns in transgenic fish. The dataset, which comprises 109 transgenic and enhancer trap lines, is described in Marquart et al Fr Neural Circuits (2015).
Download the image stacks, software and instructions from this zip file: zbb.zip
Explore the larval zebrafish brain in three dimensions, using our
Flote analyzes high speed video recordings of larval zebrafish and classifies swimming patterns for fast, high resolution analysis of larval behavior. Flote is compatible with video recordings from any camera able to record video at 1000 frames per second. Use of Flote for analyzing escape responses is described in Burgess & Granato J Neurosci (2007).
Flote downloads - Latest distribution files, including updated manual and workshop slides. To get started download flote.zip which contains the executables, and asr.zip which contains a sample image stack. PC only.
CodonZ is software for engineering coding sequences of genes for expression in zebrafish or mice. This program translates an amino acid sequence into nucleotide sequence with codons selected to match features of genes that are highly expressed. The algorithm and background are described in Horstick et al Nucl Acid Res (2015).
Note: we have a new version since the original publication with improved features. Email Harold Burgess (firstname.lastname@example.org)
CobraZ performs whole-brain voxel-intensity and deformation-field morphometry in larval zebrafish. The algorithm, validation and background are described in Gupta et al Methods (2018).
Download the software and instuctions from this zip file: cobraz.zip (83 Mb. Windows, Linux).
DAQtimer automates behavioral testing, allowing millisecond level control over stimuli and video recording from an easy to learn scripting language. DAQtimer includes commands to set analog or digital output levels, trigger high speed cameras and present video stimuli. To run DAQtimer you'll need a National Instruments PCI DAQcard or USB DAQ board.
DAQtimer FAQ - Answers to questions on using or installing DAQtimer
DAQtimer downloads - Latest distribution files. PC only.