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https://edspace.american.edu/openbehavior/project/wave-surfer/
Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus.
Proper citation: Wave Surfer project (RRID:SCR_021476) Copy
https://edspace.american.edu/openbehavior/project/caiman/
Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.
Proper citation: Calcium Imaging data Analysis project (RRID:SCR_021477) Copy
http://www.nitrc.org/projects/arts/
Software tool as automated biomarker that outputs score linked to likelihood person sufferring from arteriolosclerosis based on brain MRI data and basic demographic information. MRI data processing pipeline and classifier are packaged into software container.Users do not need to perform any image processing, and are only required to install Singularity to run ARTS.
Proper citation: ARTS biomarker (RRID:SCR_019288) Copy
https://github.com/ttrogers/DecodingDynamic
Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.
Proper citation: DecodingDynamic (RRID:SCR_021099) Copy
https://edspace.american.edu/openbehavior/project/bonvision/
Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists.
Proper citation: BonVision project (RRID:SCR_021491) Copy
The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays.
Proper citation: Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) Copy
https://edspace.american.edu/openbehavior/project/open-source-whisking-video-database/
Portal provides shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.
Proper citation: Open Source Whisking Video Database portal (RRID:SCR_021404) Copy
https://github.com/NeLy-EPFL/DeepFly3D
Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.
Proper citation: DeepFly3D (RRID:SCR_021402) Copy
https://cloudreg.neurodata.io/
Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration.
Proper citation: CloudReg (RRID:SCR_022795) Copy
https://edspace.american.edu/openbehavior/project/argus/
Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.
Proper citation: Argus (RRID:SCR_021585) Copy
https://github.com/humanlongevity/HLA
Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.
Proper citation: xHLA (RRID:SCR_022277) Copy
https://www.portal.brain-bican.org/
Provides molecular and anatomical foundational framework for study of brain function and disorders.Comprehensive Center on Human and Non-Human Primate Brain Cell Atlases with goal to build reference brain cell atlases that will be used throughout research community.
Proper citation: BRAIN Initiative Cell Atlas Network (RRID:SCR_022794) Copy
Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis.
Proper citation: Tissue Studio (RRID:SCR_023001) Copy
https://bbp.epfl.ch/nmc-portal/welcome.html
Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex. NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit.
Proper citation: Neocortical Microcircuit Portal (RRID:SCR_022032) Copy
https://www.nitrc.org/projects/qcalign
Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas.
Proper citation: QCAlign (RRID:SCR_023088) Copy
https://edspace.american.edu/openbehavior/project/mousemove/
Portal provides MouseMove software system used to analyze Open Field behavior of mice after experimental stroke to show reduced locomotor activity and to quantify laterality deficits. System is used in combination with open source program ImageJ and MTrack2 plugin to analyze pre recorded Open Field test video. System has two downloadable components, ImageJ macro and separate program with custom built MouseMove GUI. ImageJ is used to subtract background video from experiment and create image of animals total trajectory. MouseMove GUI then completes detailed analysis of movement patterns, measuring fractional time spent stationary, distance traveled, speed mean and various details of laterality.
Proper citation: MouseMove project (RRID:SCR_021581) Copy
https://www.cis.jhu.edu/~younes/CA.html
Web portal that explains technique of Diffeomorphic Mapping and Shape Analysis.
Proper citation: Generative Diffeomorphic Mapping (RRID:SCR_022825) Copy
Joint computational research center with Carnegie Mellon University and University of Pittsburgh. Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research.
Proper citation: Pittsburgh Supercomputing Center (RRID:SCR_022823) Copy
https://github.com/vesselman/SparkAn
Software tool for custom calcium imaging analysis.
Proper citation: SparkAn (RRID:SCR_022028) Copy
https://rewireneuro.com/product/pipsqueak/
Software image analysis tool as older ImageJ/Fiji plugin version.
Proper citation: Pipsqueak AI (RRID:SCR_022149) Copy
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