ViBE-Z: The Virtual Brain Explorer for Zebrafish


--> ViBE-Z Web Interface

ViBE-Z, the "Virtual Brain Explorer for Zebrafish" is an imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae.

Contents

1 ViBE-Z Overview


ViBE-Z contains a database with precisely aligned gene expression patterns (1μm^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. A detailed description of the ViBE-Z framework and its applications is provided in Ronneberger et al. (2012). A brief overview over the main parts is depicted in the following figure.

ViBE-Z overview: (a) Confocal stacks of different 72 hpf zebrafish larvae (red: nuclear stain, green: gene expression pattern). (b) ViBE-Z software and standard larva (c) Aligned patterns. (d) ViBE-Z database containing many different expression patterns (shown in different colors) precisely aligned to the standard larva. (e) ViBE-Z atlas, containing the anatomical segmentation of the standard larva.

2 ViBE-Z Database and Atlas


The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download:

File Size Date Contents
ViBE-Z_72hpf_v1.h5 218 MB 05/2012
uint8  500x500x800 /anatomy/average_brain   (element_size_um: 1,1,1)
uint8  500x500x800 /anatomy/reference_larva (element_size_um: 1,1,1)
uint8  500x500x800 /anatomy/segment_lines   (element_size_um: 1,1,1)
uint8  500x500x800 /anatomy/segment_regions (element_size_um: 1,1,1)
uint8  500x500x800 /expression/3A10         (element_size_um: 1,1,1)
uint8  500x500x800 /expression/AcTub        (element_size_um: 1,1,1)
uint8  500x500x800 /expression/TH           (element_size_um: 1,1,1)
uint8  500x500x800 /expression/dlx5a_6a_GFP (element_size_um: 1,1,1)
uint8  500x500x800 /expression/emx3_YFP     (element_size_um: 1,1,1)
uint8  500x500x800 /expression/foxd3_GFP    (element_size_um: 1,1,1)
uint8  500x500x800 /expression/glyt2_WISH   (element_size_um: 1,1,1)
uint8  500x500x800 /expression/hb9_GFP      (element_size_um: 1,1,1)
uint8  500x500x800 /expression/hcrt_EGFP    (element_size_um: 1,1,1)
uint8  500x500x800 /expression/isl1_GFP     (element_size_um: 1,1,1)
uint8  500x500x800 /expression/neurod_GFP   (element_size_um: 1,1,1)
uint8  500x500x800 /expression/nkx2.2a_GFP  (element_size_um: 1,1,1)
uint8  500x500x800 /expression/olig2_EGFP   (element_size_um: 1,1,1)
uint8  500x500x800 /expression/otpb_GFP     (element_size_um: 1,1,1)
uint8  500x500x800 /expression/tbr1b_WISH   (element_size_um: 1,1,1)
uint8  500x500x800 /expression/th_WISH      (element_size_um: 1,1,1)
ViBE-Z_48hpf_v1.h5 70 MB 05/2012
uint8  500x500x800 /anatomy/average_brain   (element_size_um: 1,1,1)
uint8  500x500x800 /anatomy/reference_larva (element_size_um: 1,1,1)
uint8  500x500x800 /anatomy/segment_lines   (element_size_um: 1,1,1)
uint8  500x500x800 /anatomy/segment_regions (element_size_um: 1,1,1)
ViBE-Z_96hpf_v1.h5 100 MB 05/2012
uint8  500x500x1000 /anatomy/average_brain   (element_size_um: 1,1,1)
uint8  500x500x1000 /anatomy/reference_larva (element_size_um: 1,1,1)
uint8  500x500x1000 /anatomy/segment_lines   (element_size_um: 1,1,1)
uint8  500x500x1000 /anatomy/segment_regions (element_size_um: 1,1,1)

2.1 Explore Database with ImageJ

To explore the database, we recommend to use ImageJ with our HDF5 plugin. After proper installation of ImageJ and the HDF plugin, and download of at least one of the database files, you can open the datasets by "File--Import--HDF5...". A multi-color overlay can be created then by "Image--Color--Merge Channels..."

Screenshot of ImageJ Software with HDF plugin Screenshot of ImageJ orthogonal slices Screenshot of ImageJ 3D Viewer

2.2 Explore Database with Matlab

The commercial software MATLAB natively supports the HDF5 format. E.g., loading the AcTub pattern and displaying a maximum intensity projection of it is done with a few commands:

a=hdf5read('ViBE-Z_72hpf_v1.h5', '/expression/AcTub');
m=max(a,[],3);
image(m'); axis image; colormap gray
Screenshot of Matlab

3 ViBE-Z Software


The full ViBE-Z software is available through a web interface that allows all interested users to use the ViBE-Z software without the need for complicated setup of own hard- and software. Some parts of the software are already available as Open Source:

The others will follow in near future.

3.1 Usage of the Web Interface

usage of ViBE-Z web interface

Please contact Olaf Ronneberger (ronneber@informatik.uni-freiburg.de) to obtain an account for the web interface.

The zerbrafish larva must be prepared, embedded and recorded according to the protocol provided in Ronneberger et al. (2012) and Rath et al. (2012). Please refer to ViBE-Z Data Preparation using ImageJ for step-by-step instructions and Vibez-Validate plugin to check wether your created HDF5 file is correct, and if the data quality is sufficient.

All 16 resulting stacks of one larva have to be stored as datasets into a single HDF5 file using the follwing naming convention of the follwing example file

File Size Date Contents
e098.h5 477 MB 12/2011
uint8  375x512x512 /step0/raw/dorsal/tile0/laserset0/channel0  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile0/laserset0/channel1  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile0/laserset1/channel0  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile0/laserset1/channel1  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile1/laserset0/channel0  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile1/laserset0/channel1  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile1/laserset1/channel0  (element_size_um: 1,0.994369,0.994369)
uint8  375x512x512 /step0/raw/dorsal/tile1/laserset1/channel1  (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile0/laserset0/channel0 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile0/laserset0/channel1 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile0/laserset1/channel0 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile0/laserset1/channel1 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile1/laserset0/channel0 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile1/laserset0/channel1 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile1/laserset1/channel0 (element_size_um: 1,0.994369,0.994369)
uint8  345x512x512 /step0/raw/ventral/tile1/laserset1/channel1 (element_size_um: 1,0.994369,0.994369)

Maximum intensity projections of these 16 stacks are shown in the following image (click on image for large version)

The sizes of your stacks and the resolution can differ from this example, but each of the datasets must contain an attribute "element_size_um", containing 3 floats: the element size in level-, in row-, and in column-direction. The ImageJ plugin creates this attribute automatically.

Using the obtained login and password, you can upload the created file via FTP

Server:vibez.informatik.uni-freiburg.de
login: (your login)
password: (your password)

Then log in to the ViBE-Z web interface at http://vibez.informatik.uni-freiburg.de/webinterface/index.php. The start page shows a list of the uploaded files, the status of the compute server, a list of completed and running jobs, and allows to create new jobs.

A new job can be added on a second page. There the files and the required processing steps are selected. If necessary, parameters of the individual modules may be adjusted.

The status of the jobs is reflected in log files.

After the job has finished, the resulting file (containing the final result as well as intermediate results for quality control) can be downloaded via FTP.

4 References


5 Contact




Last Update: 12.9.2013