• • Analize Labeler: A plug-in which extracts label names from Amira label files and writes out the label names to MBAT ,lbl files.

BrainGraph Editor

BrainGraph Editor is a JAVA applications that allows a user to create, visualize, edit, and save hierarchies

BrainGraph Editor

BrainGraph Editor is a JAVA applications that allows a user to create, visualize, edit, and save hierarchies

To Access other Tools Offered by the BIRN Community: BIRN Tools

Mouse BIRN Atlasing Toolkit (MBAT)

MBAT is designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types. Visit this page, or the MBAT BIRN download site to learn more about MBAT: RELEASE DATE 11/23/07

Mouse BIRN Atlasing Toolkit (MBAT)

MBAT is designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types. Visit this page, or the MBAT BIRN download site to learn more about MBAT: RELEASE DATE 11/23/07

Data Acquisition and Processing resources by affiliated groups:

• Processed Microarray Data: The Mouse BIRN group has developed a processed microarray data resource for the public to upload, store, and immediately visualize their own data in MBAT. This resource can be accessed from MBAT or directly on the web at http://microarray.nbirn.net/.

Additional analysis and processing resources by affiliated groups:

• Pipeline is a dataflow management and execution JAVA environment
• SHIVA is a 2D and 3D Visualization and label painting software
• BrainSuite2: Mostly human (can be used for mouse) 2D and 3D MRI visualization and processing software

• Atlas Ineroperability API: The Mouse BIRN Group has been developing an Atlas Interoperability Server and API to facilitate atlas state exchange across different atlasing tools and coordinate frames. While this is a work in progress, the Mouse BIRN group has started developing both these resources and appreciate input on improvements and future interested participants. See the Atlas State Exchange API page and the 2007 Atlas State Exchange Page, which focuses on the Atlas Interoperability Server for more information.

Search/GET commands that facilitate Microarray data integration from GeneNetwork^?

• Search WebQTL at http://www.genenetwork.org/search.html
• Access the scriptable interface (for machines) http://www.genenetwork.org/CGIDoc.html

Data:

• Visit the BIRN Data Repository to Access Data offered by the Mouse BIRN group.

Mouse BIRN Atlasing Toolkit (MBAT)

MBAT is designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types. Visit this page, or the http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT^? to learn more about MBAT: RELEASE DATE 11/23/07

• LONI Debabeler is an image data conversion resource

• The Mouse BIRN group has developed a processed microarray data resource for the public to upload, store, and immediately visualize their own data in MBAT. This resource can be accessed from MBAT or directly on the web at http://microarray.nbirn.net/.

• Pipeline is a dataflow management and execution JAVA environment
• SHIVA is a 2D and 3D Visualization and label painting software

Modified Search/GET commands that facilitate mouse BIRN integration

• Search WebQTL at http://www.genenetwork.org/search.html
• Access the scriptable interface (for machines) http://www.genenetwork.org/CGIDoc.html

• MacOStat 3D Atlas Viewer: 'MacOStat' is a digital Cryostat application designed initially to provide a real-time responsive navigational interface to high density, histologically prepared, 3D neuroanatomical data. The user interface was specifcally designed with the neuroanatomist in mind, provding a "virtual knife" tool with which the investigator slices through the digital tissue block (3D data set). The system has evolved into a full-featured viewer for any modality of 3D data stored in the macrovoxel format.
  • The 'MacOStat' program is a stand-alone Mac OS application capable of loading 3D data sets from local storage (e.g., your PC hard drive or CD/DVD drive), or via an Internet-accessible server. As a "Carbonized" application, the researcher can use 'MacOStat' both on the legacy Mac OS (OS 9), as well as the current Mac OS X operating system environment.
  • It supports arbitrary plane of view and display of both histological images and can superimpose spatially mapped, delineated regions. For detailed instructions on use, review the MacOStat Users Guide.

• 'NetOStat'(URL link pending): 'NetOStat' is a pure Java application encapsulating the client viewer functionality of 'MacOStat'. It supports nearly all the navigational tools and data display capabilities of 'MacOStat', but only provides access to 3D data sets by connecting to the Neuroterrain Atlas server over the Internet. As a platform independent Java application, it should run under any operating system environment running a modern, Java framework (JVM v1.4.x+) - e.g., Windows XP/2000, Linux, Solaris, Mac OS (Mac OS X only due to the limits of the legacy Mac OS 9 Java Virtual Machine), etc.. So far, only limited testing on platforms other than Mac OS X has been done. We ask that you please notify us of any difficulties you have running 'NetOStat', to enable us to continue to evolving it into a robust, platform-independent tool.

• ImageJ plug-in to open RAW-format volume images from the BIRN SRB-Duke

• Atlas Ineroperability API: The Mouse BIRN Group has been developing an Atlas Interoperability Server and API to facilitate atlas state exchange across different atlasing tools and coordinate frames. While this is a work in progress, the Mouse BIRN group has started developing both these resources and appreciate input on improvements and future interested participants. See the Atlas State Exchange API page and the 2007 Atlas State Exchange Page, which focuses on the Atlas Interoperability Server for more information.

Tools:

• Fido is an interactive, graphic, fiducial marking software for placing, editing, and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view and crop the tilt series. Requirements XFido: X Window and OpenGL JFido: Java and Java Web Start download through the NCMIR website.
• Voxtrace enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume while being guided by simultaneous views of the tracing displayed on a volume rendering or tilt-series. Traced contours can be viewed using XDend or used to generate surfaces for viewing in Synu. Requirements XVoxtrace: OpenGL^?, X windows, and Linux platforms JVoxtrace: Java and Java 3D, download through the NCMIR website
• Btrack analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field. Requirements: SGI IRIX and Iris GL, download through the NCMIR website

• JViewer is a 3D viewer written in Java and Java 3D and launchable via the web. It has been integrated into the BIRN Portal, the Telescience Portal, and the Cell Centered Database (CCDB). It can currently view Synu polygon mesh, Voxtrace contours, and Microbrightfield's Neurolucida V3 ASCII file formats. Requirements: Java and Java 3D, download through the NCMIR website
• Synuview/OpenSynu allows for interactive investigation of 3D volumes and the production of high-quality 3D images of the data. Synuview/OpenSynu works with polygon meshes, stacks of contour lines, or 3D volumes from confocal Z-series, tomography, or simulations. Requirements: X Window and OpenGL, download through the NCMIR website
• ImageJ Plugins: A number of ImageJ^? Plugins have been created by NCMIR computer scientists to use during the processing of large scale mosaic images including: Detailed instructions for RTS2000 mosaic processing can be found online at: http://ncmir.ucsd.edu/~skchow/rts2000/mosaicprocess.html
  • Montage RTS2000: splits an .IMG file into tiff stacks, separated by channels; option to perform a maximum projection in Z for each channel (standard processing procedure), otherwise, there will be a separate tiff stack for each Z level; option to manually adjust the size of the mosaic before the IMG file is split, used when data taking was stopped prematurely to make the file usable by the Image J plugins
  • Normalize: removes lighting gradients inherent in images produced by light microscope optics
  • MEManual Align: allows for the manual alignment of images in X and Y
  • MECombine: Stitches together tiff stacks that have undergone a maximum Z projection in the by the Montage RTS2000 plug-in and creates an image mosaic tiff; option to use an autoalignment algorithm to attempt a more precise alignment and stitching of the images.
  • Combine All: Stitches together tiff stacks that have not undergone a maximum Z projection in the by the Montage RTS2000 plug-in and creates an image mosaic tiff; option to use an autoalignment algorithm to attempt a more precise alignment and stitching of the images.
  • MERGB File Merge: combines maximum Z projected mosaic tiff files into a single RGB tiff image; user designates which channels have either a red, green or blue look up table applied.
  • RGB File Merge All: combines mosaic tiff files into a single RGB tiff image; user designates which channels have either a red, green or blue look up table applied.
  • ME Tiled Display: a mosaic navigation plug-in that allows the user to view and manipulate tile tiff mosaics .

To Access other Tools Offered by the BIRN Community: BIRN Tools

Mouse BIRN: Tools offered from the collaborative efforts of Mouse BIRN

Mouse BIRN Atlasing Toolkit (MBAT)

Visit this page to learn more about MBAT: RELEASE DATE 11/23/07

Data Acquisition and Processing Tools

• LONI Debabeler: Image data conversion

Data upload, Storage, and Management

Analysis and Processing

• Dend is an interactive program for resectioning and deriving measurements from contoured structures. It creates structural measurements obtaining lengths, surfaces, and volumes from volume data. Investigation of 3D structures and communication to others are greatly facilitated by this computer-based visualization. Requirements: X Window and OpenGL download through the NCMIR website
• Fido is an interactive, graphic, fiducial marking software for placing, editing, and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view and crop the tilt series. Requirements XFido: X Window and OpenGL JFido: Java and Java Web Start download through the NCMIR website

Visualization and Atlasing

• ImageJ plug-in to open RAW-format volume images from the BIRN SRB-Duke

Data Integration

Mouse BIRN Atlasing Toolkit (MBAT)

Visit this page to learn more about MBAT: RELEASE DATE 11/23/05

BIRN Software License

Mouse BIRN Participants: Tools offered by individual participants of Mouse BIRN

• • mask.avi: Movie of how to use BrainSuite 2 for masking the skull
  • mask.wmv: Movie of how to use BrainSuite2 for masking the skull: windows media format
  • mask.mov: Movie of how to use BrainSuite2 for masking the skull: quicktime movie format

• • label.avi: Movie of how to use BrainSuite 2 for labeling images
  • label.wmv: Movie of how to use BrainSuite2 for labeling images: windows media format
  • label.mov: Movie of how to use BrainSuite2 for labeling images: quicktime movie format

• • cleaningamask.doc: detailed methods for cleaning up a mask

Applications offered as part of the Mouse BIRN effort

Mouse BIRN: Tools offered from the collaborative efforts of Mouse BIRN

Mouse BIRN Atlasing Toolkit (MBAT)

The mouse BIRN is pleased to announce a beta version release of the Mouse BIRN Atlasing Toolkit (MBAT). It was officially released at the 2005 Society for Neuroscience Meeting and is available to everyone. The means for easy download of this tool are in process. In the meantime, if you would like to recieve a version of the tool contact Jyl Boline. Release date: 11/23/05

BIRN Software License

Applications offered as part of the mouse BIRN effort

Mouse BIRN: Tools offered from the collaborative efforts of mouse BIRN

Mouse BIRN Atlasing Toolkit (MBAT)

The mouse BIRN is pleased to announce a beta version release of the Mouse BIRN Atlasing Toolkit (MBAT). It was officially released at the 2005 Society for Neuroscience Meeting and is available to everyone. The means for easy download of this tool are in process. In the meantime, if you would like to recieve a version of the tool contact Jyl Boline. Release date: 11/23/05

Mouse BIRN viewer (MORT)

Download the new mouse BIRN viewer (MORT). Release date: 10/16/05

• mort.jar: Mouse BIRN Viewer

BIRN: Tools offered by the BIRN community: BIRN Tools

Mouse BIRN Participants: Tools offered by individual participants of mouse BIRN

Mouse BIRN

• MBAT_coronal.jpg:
  

BIRN

Download the new mouse BIRN viewer (MORT) here

• mort.jar: Mouse BIRN Viewer

• • mask.avi: Movie of how to use BrainSuite^? 2 for masking the skull
  • label.avi: Movie of how to use BrainSuite^? 2 for labeling images
  • cleaningamask.doc: detailed methods for cleaning up a mask

UTHSC

Modified Search/GET commands that facilitate mouse BIRN integration

• Search WebQTL at http://www.genenetwork.org/search.html
• Access the scriptable interface (for machines) http://www.genenetwork.org/CGIDoc.html

• SHIVA: 2D and 3D Visualization and label painting software

• BrainSuite2: Mostly human (can be used for mouse) 2D and 3D MRI visualization and processing software

Drexel

Tools:

1. MacOStat 3D Atlas Viewer: 'MacOStat' is a digital Cryostat application designed initially to provide a real-time responsive navigational interface to high density, histologically prepared, 3D neuroanatomical data. The user interface was specifcally designed with the neuroanatomist in mind, provding a "virtual knife" tool with which the investigator slices through the digital tissue block (3D data set). The system has evolved into a full-featured viewer for any modality of 3D data stored in the macrovoxel format.

   The 'MacOStat' program is a stand-alone Mac OS application capable of loading 3D data sets from local storage (e.g., your PC hard drive or CD/DVD drive), or via an Internet-accessible server. As a "Carbonized" application, the researcher can use 'MacOStat' both on the legacy Mac OS (OS 9), as well as the current Mac OS X operating system environment.

   It supports arbitrary plane of view and display of both histological images and can superimpose spatially mapped, delineated regions. For detailed instructions on use, review the user guide (URL link pending).

2. 'NetOStat'(URL link pending): 'NetOStat' is a pure Java application encapsulating the client viewer functionality of 'MacOStat'. It supports nearly all the navigational tools and data display capabilities of 'MacOStat', but only provides access to 3D data sets by connecting to the Neuroterrain Atlas server over the Internet. As a platform independent Java application, it should run under any operating system environment running a modern, Java framework (JVM v1.4.x+) - e.g., Windows XP/2000, Linux, Solaris, Mac OS (Mac OS X only due to the limits of the legacy Mac OS 9 Java Virtual Machine), etc.. So far, only limited testing on platforms other than Mac OS X has been done. We ask that you please notify us of any difficulties you have running 'NetOStat', to enable us to continue to evolving it into a robust, platform-independent tool.

Data:

• 3D Mouse Brain data set: This 3D Mouse Atlas (v2.0) is a high-resolution,17.9 micron, isotropic 3D dataset. It is composed of reconstructed Nissl stained sectional material from a freshly frozen brain of an adult male C57BL/6J strain mouse.

  In order to visualize this atlas, you must first download & install our 'MacOStat' atlas viewer application for the Macintosh OS. You can then either download this 3D Mouse atlas data set for viewing from your local hard drive or access it directly over the Internet via the Neuroterrain Atlas Server. A pure Java, platform independent client ('NetOStat') is also available. It supports nearly all the same navigational tools and data display capabilities as 'MacOStat', but only provides access to 3D data sets via connecting to the Neuroterrain Atlas server over the Internet.

  NOTE to Mouse-BIRN participants: this is the 3D histological atlas data set which will eventual contain all the regions - applied with bilaterally symmetry - from our 2D Rat Atlas. This currrent version of the 3D Mouse Atlas contains only those regions that have been directly, manually segmented on to it by our neuroanatomical staff.

Dend is an interactive program for resectioning and deriving measurements from contoured structures. It creates structural measurements obtaining lengths, surfaces, and volumes from volume data. Investigation of 3D structures and communication to others are greatly facilitated by this computer-based visualization. Requirements: X Window and OpenGL^?

Fido is an interactive, graphic, fiducial marking software for placing, editing, and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view and crop the tilt series. Requirements XFido: X Window and OpenGL^? JFido: Java and Java Web Start

Voxtrace enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume while being guided by simultaneous views of the tracing displayed on a volume rendering or tilt-series. Traced contours can be viewed using XDend or used to generate surfaces for viewing in Synu. Requirements XVoxtrace: OpenGL^?, X windows, and Linux platforms JVoxtrace: Java and Java 3D

Btrack analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field. Requirements: SGI IRIX and Iris GL

JViewer is a 3D viewer written in Java and Java 3D and launchable via the web. It has been integrated into the BIRN Portal, the Telescience Portal, and the Cell Centered Database (CCDB). It can currently view Synu polygon mesh, Voxtrace contours, and Microbrightfield's Neurolucida V3 ASCII file formats. Requirements: Java and Java 3D

Synuview/OpenSynu allows for interactive investigation of 3D volumes and the production of high-quality 3D images of the data. Synuview/OpenSynu works with polygon meshes, stacks of contour lines, or 3D volumes from confocal Z-series, tomography, or simulations. Requirements: X Window and OpenGL^?

ImageJ Plugins: A number of ImageJ^? Plugins have been created by NCMIR computer scientists to use during the processing of large scale mosaic images including:

Montage RTS2000: splits an .IMG file into tiff stacks, separated by channels; option to perform a maximum projection in Z for each channel (standard processing procedure), otherwise, there will be a separate tiff stack for each Z level; option to manually adjust the size of the mosaic before the IMG file is split, used when data taking was stopped prematurely to make the file usable by the Image J plugins

Normalize: removes lighting gradients inherent in images produced by light microscope optics

MEManual Align: allows for the manual alignment of images in X and Y

MECombine: Stitches together tiff stacks that have undergone a maximum Z projection in the by the Montage RTS2000 plug-in and creates an image mosaic tiff; option to use an autoalignment algorithm to attempt a more precise alignment and stitching of the images.

Combine All: Stitches together tiff stacks that have not undergone a maximum Z projection in the by the Montage RTS2000 plug-in and creates an image mosaic tiff; option to use an autoalignment algorithm to attempt a more precise alignment and stitching of the images.

MERGB File Merge: combines maximum Z projected mosaic tiff files into a single RGB tiff image; user designates which channels have either a red, green or blue look up table applied.

RGB File Merge All: combines mosaic tiff files into a single RGB tiff image; user designates which channels have either a red, green or blue look up table applied.

ME Tiled Display: a mosaic navigation plug-in that allows the user to view and manipulate tile tiff mosaics .

Detailed instructions for RTS2000 mosaic processing can be found online at: http://ncmir.ucsd.edu/~skchow/rts2000/mosaicprocess.html

• ImageJ plug-in to open RAW-format volume images from the BIRN SRB

• Pipeline: Dataflow management and execution environment

• SmartAtlas and SmartAtlas tutorial: The Smart Atlas is a web-based tool based on a vector-based brain atlas for examining spatial relationships among brain structures and for integrating distributed, multi-scale data that has been registered to the atlas coordinate system.

• Pipeline version 3: Image processing and registration

• Pipeline version 3: Image processing

• Pipeline version 3: Image processing

• SHIVA: Visualization

• BrainSuite2: Mostly human (can be used for mouse) MRI visualization and processing

• LONI Debabeler: Image data conversion

Applications offered as part of the mouse BIRN effort

BIRN

Tools offered by the BIRN community: BIRN Tools

Caltech

Duke

UCLA

Visualization: SHIVA:

Additional resources: Mostly human (can be used for mouse) MRI visualization and processing: BrainSuite2:

Image data conversion: LONI Debabeler:

UCSD

UTHSC, Drexel, and BIDMC