Software
Downloads for software published by the Burgess lab at NICHD. It's all free and you are also welcome to the source code (email: burgessha@mail.nih.gov).
- Updates: If you'd like an email when we release new versions of any of these packages, subscribe here .
- Installation: These packages require you to have the free IDL virtual machine installed on your computer. Help on installing IDL is at the bottom of this page.
Brain Browser
The Zebrafish Brain Browser allows visualization and searching of 3D expression patterns in transgenic fish. The most recent dataset, which comprises 264 transgenic and enhancer trap lines, is described in Tabor et al eLife 2019;8:e42687
Access the online version , or download the desktop version of ZBB2.0 with image stacks, software and instructions from Zenodo (5.9 GB; PC, Mac, Linux).
More information, and detailed protocols are available here: Brain Browser.
Virtual Reality Fish Brain
Explore the larval zebrafish brain in three dimensions, using our virtual reality Brain Browser app for cardboard : brainbrowser.apk (APK 42 MB) (Android only for now). With the VR brain browser you can fly into the brain of the fish, visualizing the spatial relationships between anatomically defined brain regions and gene expression patterns. Use the cardboard button to toggle movement, and to select regions from a panel floating below the brain of the fish.
Flote
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
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) .
Download the software and instructions from this zip file: CodonZ.zip (ZIP 567 KB) (PC only). Optimized genes are available from Addgene .
Note: we have a new version since the original publication with improved features. Email Harold Burgess (haroldburgess@mail.nih.gov)
CobraZ
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 (ZIP 83 MB) (Windows, Linux).
DAQtimer
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 downloads - Latest distribution files. PC only.
Help with installing IDL
All the above software runs as IDL virtual machine code. The IDL virtual machine is part of the IDL download, which is available from Harris Geospatial . You do not need to purchase an IDL license, but you do need a full IDL install, because this includes the virtual machine. Steps:
- Register for an account with Harris Geospatial , then login
- Select 'My Account' -> 'Downloads', then the latest version of IDL suitable for your operating system.
- Before download, you'll likely be blocked by a message saying 'Verification Pending'.
- If you do not receive a verification email within 24 hours, email support@exelisvis.com and request download access.
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