Contents
NCMIR develops post data-collection computer-aided image analysis resources and computer graphics tools. Computational tools available for download include applications for electron microscopic tomography, large-field light microscopy, visualization, file format conversion, specialized plug-ins, and grid computing tools. These software tools are used for computer graphics and image processing to delineate biological structures, including the derivation of contours, their editing, exploration of semi-automatic contouring, and volumetric contouring. NCMIR software can be obtained without Scientific Advisory Board approval. If you have questions or need additional information call (858) 534-0276.
Visualization
Cytoseg
Cytoseg -- by: Rick Giuly
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An open source project for automatic segmentation of neuropil. The goal of the Cytoseg project is to build tools that reduce the manual labor involved with segmentation of nueropil. Modules under development include automatic contour detectors for mitochondrion, vesicle, and cytosol regions. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools). Cytoseg is currently in a pre-alpha stage.
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Jinx
Jinx -- by: Stephan Lamont
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Jinx is a tool for segmentation of 3D data sets. It was designed specifically for 3D electron microscopic data sets produced using electron tomography, but may be used for any aligned 3d data set. It is written in Java as a Java Webstart application. Jinx contains the facility for annotating 3D microscopic data using formal ontologies. The current version of Jinx allows the choice of ontologies, including the Neuroscience Information Framework (NIF) ontologies, which includes an extensive ontology for subcellular anatomy of the nervous system based on our Subcellular Anatomy Ontology (SAO)
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WinSage
WinSage -- by: Raj Singh
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SAGE is a graphics streaming architecture for supporting high-resolution, scalable and collaborative scientific visualization environments with potentially hundreds of megapixel of contiguous display resolution. It is primarily designed to be run as a thin middleware on cluster driven tile-displays. It allows users to treat the high-resolution distributed displays as one contiguous desktop where users can move/resize application windows. SAGE is network centric and the applications running on these displays need not run locally. The applications can be run on remote machines or clusters and can stream their pixel framebuffers to SAGE enabled tile-displays.
The group responsible for the core development is at the Electronic Visualization Laboratory at the University of Illinois at Chicago.
Primary SAGE website: [http://www.evl.uic.edu/cavern/sage/].
This webpage supports the Windows 32-bit versions of software used for building and configuring scalable tile-displays. The Windows port was done at the National Center for Microscopy and Imaging Research under a grant by Microsoft Research. The software has been tested on Windows XP based tile-displays driven by a high-bandwidth backplane (1Gpbs) and bundles in SAGE application binaries/source for remote presentation, large 2D/3D dataset visualization and HD video playback and streaming amongst others.
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The group responsible for the core development is at the Electronic Visualization Laboratory at the University of Illinois at Chicago.
Primary SAGE website: [http://www.evl.uic.edu/cavern/sage/].
This webpage supports the Windows 32-bit versions of software used for building and configuring scalable tile-displays. The Windows port was done at the National Center for Microscopy and Imaging Research under a grant by Microsoft Research. The software has been tested on Windows XP based tile-displays driven by a high-bandwidth backplane (1Gpbs) and bundles in SAGE application binaries/source for remote presentation, large 2D/3D dataset visualization and HD video playback and streaming amongst others.
Data Reconstruction & Analysis
APIs (8-9 jar files)
APIs (8-9 jar files) -- by: Asif Memon
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This software enables client applications to communicate with remote map servers that serve 2D brain data. The Java wrapper supports requesting images or image fragments from these servers, taking as input the image server address, respective service name, and image fragment coordinates. The coordinates are expected to follow a coordinate system of the image as recorded in spatial registry. It is also expected that the image is warped to a canonical reference space, and registered to one of pre-defined coordinate systems (e.g. ABA reference plates, Paxinos and Watson reference plates).
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Image J Mosaic Plugins
Image J Mosaic Plugins -- by: Sunny Chow & Hiroyuki Hakozaki
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This package contains plugins for ImageJ to create large scale mosaic images. It supports images taken with NCMIR customized microscopes RTS2000 from Bio-rad and FluoView 1000 from Olympus. These instruments acquire images of a large area by moving motorized stage automatically. This plugins package support manual image offset alignment, automated image offset calculation, image normalization, combine images based on alignment information and merge three channel combined image in RGB color. Although this module is written in Java, there is platform dependency and we currently only support the Windows platform. It has been tested on Windows XP Professional and Windows Vista.
Details of image processing description is published in following paper: Automated microscopy system for mosaic acquisition and processing. S. K. CHOW, H. HAKOZAKI, D. L. PRICE, N. A. B. MACLEAN, T. J. DEERINCK, J. C. BOUWER, M. E. MARTONE, S. T. PELTIER & M. H. ELLISMAN, Journal of Microscopy Volume 222 Issue 2, Pages 76 - 84
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INCF
INCF -- by: Asif Memon
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This collection of web services supports access to several online digital atlases. In the current version, the atlases include the Allen Brain Atlas, the Edinburgh Mouse Atlas Project (EMAP), brain images available registered in the UCSD spatial registry and CCDB, and the WHS (Waxholm Space) reference atlas. Each service supports a GetCapabilities and DescribeProcess requests which describe functionality of the service. Each service also contains a set of spatial translations that support coordinate transformations between the WHS space and the coordinate spaces used by individual atlases (including conversions between WHS and ABA voxel space, ABA reference plates, AGEA, and Paxinos/Watson reference plates.) In addition, each service may expose atlas-specific functionality. For example, the service exposing functionality of the Allen Brain Atlas would contain such requests as GetCorrelationMapByPOI, Get2dImageByPOI, GetGenesByPOI, each of them taking coordinates of a point of interest as input.
The services are designed to be called remotely, and are currently called from a 3D atlas integration client developed at UCSD. The services are a component of the digital atlasing infrastructure (DAI) being promoted by INCF, and are initially developed to support INCF-DAI demonstration at Neuroinformatics'2009.
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The services are designed to be called remotely, and are currently called from a 3D atlas integration client developed at UCSD. The services are a component of the digital atlasing infrastructure (DAI) being promoted by INCF, and are initially developed to support INCF-DAI demonstration at Neuroinformatics'2009.
TxBr
TxBr -- by: Rick Lawrence, Alex Kulongowski and Sebastien Phan
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TxBR is a an advanced electron tomography code. This code contains alignment, image correction, filtering and backprojection reconstruction modules. Special features include alignment from projected contours of structures in the object, which reduces or eliminates the need for special markers; image and reconstruction dewarping, which increase the accuracy of the reconstruction and allows for high-quality montaging and z-stacking of reconstructions; generalization of the projection model, which permits a wide range of data acquisition protocols; and parallel versions, which permit the use of the code on parallel machines, computer clusters and graphics processor boards.
This code is uniquely suited for the processing of wide field Electron Microscope images and tilt series, produces graphical diagnostic output at each step and is almost completely automated beyond the tracking or contour marking steps. It has been rigorously tested over a wide range of electron microscope instrumentation, computer hardware, and biological data sets. Wiki information on the scientific basis of the code and instructions for its use may be found on the NBCR web site. Documentation
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This code is uniquely suited for the processing of wide field Electron Microscope images and tilt series, produces graphical diagnostic output at each step and is almost completely automated beyond the tracking or contour marking steps. It has been rigorously tested over a wide range of electron microscope instrumentation, computer hardware, and biological data sets. Wiki information on the scientific basis of the code and instructions for its use may be found on the NBCR web site. Documentation
File Format Converter
Convertilizer
Convertilizer -- by: Stephan Lamont
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Convertilizer is a tool for converting between sundry volume and image formats commonly used at NCMIR, including IMOD, Suprim, Analyze 7.5, and TIFF. It can produce image stacks, where the format permits, or take apart an image stack into separate files. It also has a facility for making Quicktime (.MOV) movies from stacks or series of images.
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Instrumentation Control & Automation
8k Camera code
8k Camera code -- by: Yukiko Hakozaki
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This software supports controlling and image acquisition of 4Kx4K CCD camera from Spectra Instruments. It is a Microsoft COM module and client software can bind to this module dynamically at run time. This module support only the Windows platform. It has been tested on Windows XP Professional SP2.
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Serial EM
Serial EM -- by: Boulder Labs
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SerialEM was developed by the Boulder Laboratory for 3-Dimensional ELectron Microscopy of Cells ("BL3DEMC") at the University of Colorado. The commercial version of the 4k camera was integrated into SerialEM.SerialEM is a Windows based program used to acquire tilt series for electron tomography on FEI and JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. It does not count on the microscope or the specimen being particularly well-behaved, so unless a prediction appears reliable, it falls back to measuring and adjusting defocus and/or specimen position when necessary. With this method, it achieves both the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the speed of the newer precalibration approach. A 2Kx2K, 1 degree tilt series can be acquired in about 45 minutes with a single-port readout camera or 20-25 minutes with a four-port readout camera.
The commercial version of the NCMIR 4k x 4k lens coupled camera can be downloaded here.
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The commercial version of the NCMIR 4k x 4k lens coupled camera can be downloaded here.
Telemicroscopy
Telemicroscopy -- by: Tomas Molina
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A .NET based software application was developed to remotely control NCMIR’s Jeol 3200 energy filtered electron microscope. COM packages were written to “wrap” instrument and imaging control around the microscope so as to easily expose control as simple interfaces within a C# application. Users can manipulate such parameters as magnification, brightness, focus, and condenser beam shifts. Users can also manipulate the goniometer of the electron microscope by changing such parameters as x,y,z, and tilting the specimen from \-60 to \+60 degrees. Real time video of the screen image of the microscope is provided along with a 4k x 4k high resolution image provided by our CCD cameras. Users are able to mouse click on various locations of the x,y stage and can quickly navigate large areas for surveying the specimen of study. The .NET Telemicroscopy C# application was demonstrated at SuperComputing.
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Database & Data Mangement
CCDB Portlets
CCDB Portlets -- by: Willy Wong
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The MyCCDB portal is community software for managing and sharing high resolution light and electron microscopic data. The CCDB divides the process of data entry into different stages, each with its own set of data input forms.
1) Microscopy Product Registration form assigns a unique ID to each “microscopy product”. The microscopy product is used to describe a set of related images. These images may be related in a systematic way, e.g., tilt series, optical section series, serial section, time series, mosaic, or they may be a set of survey images that were taken of the same specimen at the same time. The microscopy product ID serves as the accession number for a data set. Microscopy product ID’s can be obtained before any imaging data is acquired. Because the ID is unique, any data products labeled with this ID, e.g., negatives, can be associated with the appropriate set of details.
2) This Detailed Data input form handles the data input for more detailed data of a microscopy product, such as imaging information reconstruction and segmentation data... and it also provides users with the ability to upload data files for the datasets. Users will be able to select a pre-registered microscopy product and create a detailed dataset from the existing microscopy product.
3) The detailed Specimen Preparationform can be used to define a structured protocol recording the steps used to prepare a specimen in the order in which they were performed. It is also required for assigning a molecular localization or stain to a particular channel for light microscopy. The specimen preparation forms are still in beta testing, i.e., they are not considered production level, but should be used in order to provide feedback for the final production release.
4) The CCDB upload Tool allows users to upload multiple types of files at once into multiple forms, rather than having to upload each file individually. The tool also will recognize file types if they are named according to the CCDB naming convention and place them in the correct fields.
If your laboratory needs a data management tool for the light and electron microscopic data, the MyCCDB portal is a open source software for you to use or to extend.
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1) Microscopy Product Registration form assigns a unique ID to each “microscopy product”. The microscopy product is used to describe a set of related images. These images may be related in a systematic way, e.g., tilt series, optical section series, serial section, time series, mosaic, or they may be a set of survey images that were taken of the same specimen at the same time. The microscopy product ID serves as the accession number for a data set. Microscopy product ID’s can be obtained before any imaging data is acquired. Because the ID is unique, any data products labeled with this ID, e.g., negatives, can be associated with the appropriate set of details.
2) This Detailed Data input form handles the data input for more detailed data of a microscopy product, such as imaging information reconstruction and segmentation data... and it also provides users with the ability to upload data files for the datasets. Users will be able to select a pre-registered microscopy product and create a detailed dataset from the existing microscopy product.
3) The detailed Specimen Preparationform can be used to define a structured protocol recording the steps used to prepare a specimen in the order in which they were performed. It is also required for assigning a molecular localization or stain to a particular channel for light microscopy. The specimen preparation forms are still in beta testing, i.e., they are not considered production level, but should be used in order to provide feedback for the final production release.
4) The CCDB upload Tool allows users to upload multiple types of files at once into multiple forms, rather than having to upload each file individually. The tool also will recognize file types if they are named according to the CCDB naming convention and place them in the correct fields.
If your laboratory needs a data management tool for the light and electron microscopic data, the MyCCDB portal is a open source software for you to use or to extend.
CCDB Schema
CCDB Schema -- by: Willy Wong
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The current schema contains over 100 tables which include experimental, imaging, and reconstruction details as well as the results of any analysis of morphological and protein localization data. An overview of the schema organization is shown. All steps of 3D reconstruction are modeled in the database, from specimen preparation to the final analysis. The images are stored separately from the descriptive data, using the Storage Resource Broker for storage and retrieval of the image data sets. Oracle was chosen as a platform because its Object Relational modeling capability allows us to program any analysis or data comparison methods into the database itself. This functionality allows us to move beyond simple retrieval queries to allow us, for example, to create a “compare two protein distributions” function that runs as an integral method from within the database.
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Collaborative Portlets
Collaborative Portlets -- by: Ramil Manansala
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The Collaboration Portlet provides a shared collaborative environment for exchanging data, conducting research studies, and providing access to shared resources. The following are some of the tools included in the portlet module; the Projects appplication is a tool intended to encapsulate a specific research activity, while the Forums facilitate online discussions. Another tool is the Blog application which gives researchers ability to create journal, news feed, and release announcements. The Lists program provides mechanism for scientists to share information on resources. Other communication tools such as Email and Chat are also provided to facilitate group communication.
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Data Grid Browser
Data Grid Browser -- by: Abel Lin
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(DESCRIPTION HERE)
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Image Server
Image Server -- by: Asif Memon
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This software enables client applications to communicate with remote map servers that serve 2D brain data. Currently, the servers include ESRI ArcIMS Server and the open source Minnesota MapServer. The Java wrapper supports requesting images or image fragments from these servers, taking as input the image server address, respective service name, and image fragment coordinates. The coordinates are expected to follow a coordinate system of the image as recorded in spatial registry. It is also expected that the image is warped to a canonical reference space, and registered to one of pre-defined coordinate systems (e.g. ABA reference plates, Paxinos and Watson reference plates). The software is downloadable as a single jar file. It is intended to be incorporated in a client application. In addition, both the spatial registry and servers are exposed as web services.
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Mediator
Mediator -- by: Vadim Astakhov
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System consists of a data integration server; an API for schema registration, view definition and query building;clients for registration, view definition and query composition; clients for semantic data mapping and query; a number of domain-specific clients that have incorporated access to the data integration environment (e.g. the Mouse BIRN Atlas Tool); and a set of tree\- and graph-structured ontologies and ontology-data mappings. The latter provides the necessary semantic information, tied to external ontologies, so that integrated queries can be executed across the sources.In the current global as view (GAV) setting of the system, the burden of creating proper integrated views over data sources is on the integration specialist who works with the domain scientists to capture the requirements of the application at hand. This often leads to the pragmatic problem that the relationships between attributes disclosed by different sources and between data values are, quite often, not obvious. To account for this, the system has created additional mapping relations. Currently there are three kinds of mapping relations.
1) The ontology-map relation that maps data-values from a source to a term of a recognized ontology.
2) A joinable relation links attributes from different relations if their data types and semantic types match. We have also developed a Concept Mapping client to assist in the creation of mapping entries in the term-index-source (TIS) at the time of source registration. The data integration environment has a specific source called the term-index-source that maintains a mapping between data from registered sources and ontological terms defined in various ontologies.
3) The value-maprelation maps a Mediator-supported data value or a Mediator-supported attribute-value pair to the equivalent attribute-value pair disclosed by the source.
For example, the Mediator may disclose a demographic attribute called "gender" with values (male, female), while a source may refer to "sex" with values (0, 1), while another source, with its own encoding scheme may call it "kcr_s57" with values (m, f). This is used by the system to preprocess queries.
TIS is a relational database and programmatic API which provide mechanism for mapping distributed data to standard ontological concepts.
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1) The ontology-map relation that maps data-values from a source to a term of a recognized ontology.
2) A joinable relation links attributes from different relations if their data types and semantic types match. We have also developed a Concept Mapping client to assist in the creation of mapping entries in the term-index-source (TIS) at the time of source registration. The data integration environment has a specific source called the term-index-source that maintains a mapping between data from registered sources and ontological terms defined in various ontologies.
3) The value-maprelation maps a Mediator-supported data value or a Mediator-supported attribute-value pair to the equivalent attribute-value pair disclosed by the source.
For example, the Mediator may disclose a demographic attribute called "gender" with values (male, female), while a source may refer to "sex" with values (0, 1), while another source, with its own encoding scheme may call it "kcr_s57" with values (m, f). This is used by the system to preprocess queries.
TIS is a relational database and programmatic API which provide mechanism for mapping distributed data to standard ontological concepts.
SRB Portlets
SRB Portlets -- by: Ramil Manansala
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The SRB Portlets is a web based interface to interact with the Storage Resource Broker. The web application support common SRB functionality including but not limited to navigation of folders and files, uploading and downloading data, adding metadata, granting folder and file permissions, as well as launching external tools for viewing and analyzing data. The portlet uses familiar desktop paradigms to enhance user experience.
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