Mouse BIRN Resources
This section contains information about the following topics:
- MouseBIRN Tools - Overview of and links to current tools offered by mouse BIRN participants
- MouseBIRN Data - Data available for download from mouse BIRN participants
- MouseBIRN Data Management - Data management tools available for download from mouse BIRN participants
- MouseBIRN Tutorials - Tutorials and Workflows available for download from mouse BIRN participants
- MouseBIRN Methods - Methods used by some of the mouse BIRN participants
Tools
Mouse BIRN Atlasing Toolkit (MBAT)
The mouse BIRN is pleased to announce a beta version release of the Mouse BIRN Atlasing Toolkit (MBAT). The original version was officially released at the 2005 Society for Neuroscience Meeting and is available to everyone. MBAT Version 2.0 was release Date 10/13/2007. You can download MBAT at http://mbat.loni.ucla.edu/
Tools offered by the BIRN community
Duke
- ImageJ - plug-in to open RAW-format volume images from the BIRN SRB
UCLA
- Pipeline: Dataflow management and execution environment
- SHIVA: 2D and 3D Visualization and label painting software
Data Sharing
Data Sharing PolicyVersion 1.0, November 2005
Data will be openly shared and made available with no restrictions other than subject confidentiality.
- Data users should cite data contributors and reference the corresponding BIRN accession number(s).
- To maintain the protection of human subjects, you agree not to attempt in any way to discover the identity of any of the human subjects.
Shared Data
BIRN shared resources can be
found at the following site http://www.nbirn.net/
Resources/Downloads/.
Tutorials
Download Version 1 of the LONI Pipeline and it's help manual
- pipelinev1_use.zip: Version 1 of the LONI Pipeline (zipped)
- LONI_Pipeline.pdf: Version 1 help manual
Download the actual Pipelines for processing the MRI images
Tutorial for processing MRI images
- mousetutorial.pdf: Tutorial for using the Pipeline and other tools to process and register mouse brain MRI images
- movies.ZIP
Methods
These are some of the multiscale mouse brain imaging protocols used by the members of the mouse BIRN.
MR Microscopy (Submitted by G. Allan Johnson)
The Center for In Vivo Microscopy (CIVM) at Duke University
All scans are performed at 9.4 T using a 1 cm solenoid rf coil. All scans are acquired in a single setting so the data sets are registered.
All scans are acquired with a fixed field of view of 11x11x22 mm with a matrix of 256x256x512 yielding voxels of 0.043x0.043x0.043 mm i.e. 8 x 10-5 mm3.
We acquire three registered data sets using standard 3DFT spin warp encoding. The TR and NEX have been adjusted so that each set will require 14.56 hrs:
- Data set A: T1 weighted @ TR=100 ms, TE=5.5 ms, Bandwidth ±31.25 kHz, NEX=8.
- Data set B: T2 weighted @ TR=200 ms, TE- 20 ms, Bandwidth ±15.62 kHz,NEX=4.
- Data set C: Spin density @ T2 weighted @ TR=200 ms, TE- 5.5 ms, Bandwidth ±15.62 kHz,NEX=4.
Histology (Submitted by Allan MacKenzie-Graham)
The Laboratory of Neuro Imaging (LONI) at the University of California at Los Angeles
After removal from the skull, the brains are dipped in 5% gelatin (Sigma) to maintain the integrity of the tissue after sectioning. The brains are then embedded in OCT compound (Sakura) at 4° C with dry ice.
Once the samples are prepared, the brains are attached to a chuck with OCT compound (Sakura), and sections are cut serially in 50µm thick sagittal sections on a modified CM3050S cryostat (Leica). A DMCIe digital camera (Polaroid) captures images of the blockface prior to each section at a resolution of 1600 x 1200 (approximately 6.7µm/pixel) in 24-bit color. Sections 200µm apart are Nissl-stained (Thionin) and alternating sections 200µm apart are myelin-stained using a modified myelin impregnation stain. Stained preparations are digitized using a 0.5X objective on an AX70 microscope (Olympus) with a DMCIe digital camera (Polaroid) at a resolution of 1600 x 1200 (approximately 6.1µm/pixel) in 24-bit color. The images are acquired using a macro imaging system that provides undistorted high-resolution images with even illumination across the entire field of view.
