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https://www.nest-initiative.org

Incorporated as non-profit member based organization promoting scientfic collaboration in computational neuroscience.Advances computational neuroscience by pushing limits of large scale simulations of biologically realistic neuronal networks.

Proper citation: NEST Initiative (RRID:SCR_020978) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/brainglobe/

Project is related to working with atlas data from multiple species on common platform.Provides collection of Python tools for working with atlas data from multiple species on common platform and for morphological analyses in systems neuroscience.

Proper citation: BrainGlobe project (RRID:SCR_021481) Copy   

•   Source: SciCrunch Registry

https://github.com/berenslab/mini-atlas

Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature.

Proper citation: BarensLab Mini-Atlas (RRID:SCR_021115) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/toolboxes-ephys-analysis/

Portal includes compared several toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, and generalized linear modeling. Discussion about major features of software available for Python and MATLAB including Brainstorm, Chronux, Elephant, FieldTrip, gramm, Spike Viewer, and SPIKY. They include succinct tables for assessing system and program requirements, quality of documentation and support, and data types accepted by each toolbox.

Proper citation: Toolboxes for Spike and LFP Analysis project (RRID:SCR_021478) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/scintillate/

Project related to time series calcium imaging evaluation and pre-processing. Included open source graphical viewer for time series calcium imaging evaluation and pre-processing is provided by Swedish University scientists .

Proper citation: Scintillate project (RRID:SCR_021479) Copy   

•   Source: SciCrunch Registry

https://ultra-dd.org

Project aim is to identify and validate novel targets in auto immune and inflammatory diseases. Used to create and profile target directed chemical and antibody probes in patient cell derived assays, provide biomarker and phenotypic read outs in more disease relevant context.

Proper citation: ULTRA-DD (RRID:SCR_018995) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.biocompare.com/19333-Image-Analysis-Software-Image-Processing-Software/4378970-Definiens-Tissue-Studio/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry