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http://www.knossostool.org/

Software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity. By dynamically loading only data from the surround of the current view point, seamless navigation is not limited to datasets that fit into the available RAM but works with much larger dataset stored in a special format on disk. Currently, KNOSSOS is limited to 8-bit data. In addition to viewing and navigating, KNOSSOS allows efficient manual neurite annotation (''skeletonization''). KNOSSOS is being used mostly for reconstructing cell morphologies from 3D electron microscopic data generated by Serial Block-Face Electron Microscopy (SBEM), with an occasional application to 2-photon and confocal optical microscopy data.

Proper citation: KNOSSOS (RRID:SCR_003582) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/

TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux.

Proper citation: TrackVis (RRID:SCR_004817) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/clever-sv/

A collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.

Proper citation: CLEVER Toolkit (RRID:SCR_005255) Copy   

•   Source: SciCrunch Registry

http://ingap.sourceforge.net/

Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations.

Proper citation: inGAP (RRID:SCR_005261) Copy   

•   Source: SciCrunch Registry

http://www.ridom.de/traceedit/

A cross-platform graphical DNA trace viewer and editor that displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate on Windows and UNIX platforms.

Proper citation: Ridom TraceEdit (RRID:SCR_005568) Copy   

•   Source: SciCrunch Registry

http://snap.cs.berkeley.edu/

A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

Proper citation: Scalable Nucleotide Alignment Program (RRID:SCR_005501) Copy   

•   Source: SciCrunch Registry

https://github.com/dsturg/Spanki

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

Proper citation: Spanki (RRID:SCR_004469) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry

http://www.brainvoyager.com/products/braintutor.html

A free award-winning educational program that teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex. The program runs on Windows XP, Vista and Windows 7.

Proper citation: BrainVoyager Brain Tutor (RRID:SCR_006737) Copy   

•   Source: SciCrunch Registry

http://www.mitk.org/DiffusionImaging

A selection of image analysis algorithms for the processing of diffusion-weighted MR images. Features & Highlights * Tensor and q-ball reconstruction * Glyph visualization * Quantification and partial volume clustering of tensor and q-ball images * Global fiber tractography, visualization, and tract post-processing * Brain network statistics and visualization (connectomics) * Interactive exploration of Tract-based spatial statistics (TBSS) results * Intra-voxel incoherent motion (IVIM) estimation * Synthetic data generation Additional system specific requirements: * Windows: If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: 32 bit or 64 bit * Linux: the Qt framework, version 4.6.2 or later Tested systems: Windows 7, Windows Vista; Ubuntu 12.04 and newer; OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion) The OS X 10.6 installer is compatible with OS X 10.7 (Lion) so there is no dedicated disk image build under 10.7. The MITK Diffusion application is based on the MITK research platform and the most of it is open-source. The available code is embedded into the source code of MITK as a module and can be accessed through the public git repository.

Proper citation: MITK Diffusion (RRID:SCR_006846) Copy   

•   Source: SciCrunch Registry

http://www.brainvoyager.com/products/brainviewer.html

Software that supports browsing and inspecting essential BrainVoyager data files as well as the header and content of DICOM files. The Viewer supports standard image files (JPEG, GIF, PNG, TIFF, BMP) allowing to inspect snapshots, figures or photos. Users can prepare a folder with selected data of a subject (VMRs, SRFs, Maps, snapshot images), which allows participants of fMRI measurements to browse their brain data and to show it to others. The Viewer can be handed over to colleagues not having a BrainVoyager license together with relevant data. This will allow them to view and explore your analyzed data files.

Proper citation: BrainVoyager Brain Viewer (RRID:SCR_006755) Copy   

•   Source: SciCrunch Registry

http://www.ebire.org/hcnlab/software/vamca.html

A stand-alone, open source human cortical meta-analysis and visualization toolbox for MatLab. It projects stereotaxic coordinates to a mean cortical surface by using an anatomical database of 60 young adults to provide multiple mappings of normalized cortical surfaces into MNI space. VAMCA performs the following analyses: # Multi-Fiducial Projection Mapping: Map stereotaxic 3D coordinates to the normalized cortical location for each of 60 database subjects. # Computing Centroid Locations for groups of foci both on a mean cortical surface and in MNI space. # Comparing Two Groups of Foci for differences in location (surface or 3D) of their group centroids and computing the groups' overlap extent using permutation tests. # Detecting Significant Densities of Foci or Density Differences of Two Groups within anatomical ROIs on a mean cortical surface by using Monte Carlo analyses. Coordinate weights allow fixed or random effects type analyses.

Proper citation: VAMCA (RRID:SCR_007028) Copy   

•   Source: SciCrunch Registry

http://dataup.cdlib.org/

An open source tool to help researchers document, manage, and archive their tabular data that integrates with Microsoft Excel. The tool will parse .xlsx or .csv file to detect the presence of potential issues that do not comply with data management best practices, assign a unique identifier to a data set and deposit it within the DataONE repository system.

Proper citation: DataUp (RRID:SCR_006905) Copy   

•   Source: SciCrunch Registry

http://mcx.sourceforge.net/

A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470.

Proper citation: Monte Carlo eXtreme (RRID:SCR_007001) Copy   

•   Source: SciCrunch Registry

http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/BrainParser

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DTIProcess

A DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess, et al..

Proper citation: DTIProcess ToolKit (RRID:SCR_009561) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cogicat/

While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage.

Proper citation: Subject Order-Independent Group ICA (RRID:SCR_009514) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/map3d.html

A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.

Proper citation: map3d (RRID:SCR_009628) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/brainmask/

Segmentation of the brain from three-dimensional MR images is a crucial pre-processing step in morphological and volumetric brain studies. BrainMask implements a fully automatic brain segmentation algorithm that uses advanced thresholding with morphology and 3D edge detection algorithms. BrainMask demonstrates high segmentation accuracy. For a representative 26 datasets, the segmentation error averaged 3.4% ������ 1.3% (Mikheev A et al. J Magn Reson Imag 27(6):1235-41;2008). BrainMask includes NNN - a tool based on the algorithm developed by John Sled for correcting the intensity non-uniformity in MR data (Sled JG et al. IEEE Trans Med Imag 17(1):87-97;1998). BrainMask also includes a versatile DICOM wiewer and allows to selectively load and organize DICOM images into 3D and 4D datasets.

Proper citation: BrainMask Volume Processing Tool (RRID:SCR_009538) Copy   

•   Source: SciCrunch Registry