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http://apps.cytoscape.org/apps/cluepedia

Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments.

Proper citation: CluePedia Cytoscape plugin (RRID:SCR_015784) Copy   

•   Source: SciCrunch Registry

https://en.freedownloadmanager.org/Windows-PC/Flowing-Software-FREE.html

Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc.

Proper citation: Flowing Software 2.5.1 (RRID:SCR_015781) Copy   

•   Source: SciCrunch Registry

https://biccn.org

Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.

Proper citation: BICCN (RRID:SCR_015820) Copy   

•   Source: SciCrunch Registry

https://zenodo.org/record/167621

Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation.

Proper citation: BeatBox (RRID:SCR_015780) Copy   

•   Source: SciCrunch Registry

http://mrir.med.miami.edu:8000/midas

Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a "whole-brain" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MIDAS (RRID:SCR_015704) Copy   

•   Source: SciCrunch Registry

http://www.biovoxxel.de/

Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis.

Proper citation: BioVoxxel Toolbox (RRID:SCR_015825) Copy   

•   Source: SciCrunch Registry

http://alleninstitute.github.io/dipde/

Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.

Proper citation: DiPDE (RRID:SCR_015822) Copy   

•   Source: SciCrunch Registry

http://www.fsm.ethz.ch/publications-list/software.html

Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.

Proper citation: FiberApp (RRID:SCR_015826) Copy   

•   Source: SciCrunch Registry

https://portals.broadinstitute.org/cmap/

Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Connectivity Map 02 (RRID:SCR_015674) Copy   

•   Source: SciCrunch Registry

https://www.licor.com/bio/image-studio/

Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself.

Proper citation: LI-COR Image Studio Software (RRID:SCR_015795) Copy   

•   Source: SciCrunch Registry

http://www.adobe.com/products/audition.html

Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes.

Proper citation: Adobe Audition (RRID:SCR_015796) Copy   

•   Source: SciCrunch Registry

https://github.com/hpardoe/napr/

Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3.

Proper citation: NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) Copy   

•   Source: SciCrunch Registry

http://www.braincode.ca

Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Proper citation: Brain-CODE (RRID:SCR_015877) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/canu

Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Proper citation: Canu (RRID:SCR_015880) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4444202

Software for high-throughput gene expression and genotyping analysis for use with the Applied Biosystems® 7900HT Fast Real Time PCR System. It features automation software tools to fully automate high-throughput applications for gene expression and SNP genotyping.

Proper citation: Sequence Detector System (RRID:SCR_015806) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/ND-3300

Fluorospectrometer for broad spectrum fluorescence analysis. It uses as little as 1 μL of sample volume and lowers the mass detection limit more than an order of magnitude.

Proper citation: NanoDrop 3300 Fluorospectrometer (RRID:SCR_015804) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4376600

Equipment and software system that is a real-time thermal cycler for intuitive data analysis of polymerase chain reactions. It comes with analysis software, instrument control software, and a LED-based 4-color optical recording feature.

Proper citation: Thermo Fisher: StepOnePlus Real-Time PCR System (RRID:SCR_015805) Copy   

•   Source: SciCrunch Registry

https://github.com/cerebis/sim3C/tree/0.1

Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities.

Proper citation: Sim3C (RRID:SCR_015772) Copy   

•   Source: SciCrunch Registry

https://www.norpix.com/products/streampix/streampix.php

Software for digital video camera recording that allows users to control and acquire dadta from multiple cameras simultaneously in a singleuser interface. StreamPix provides a complete management console for cameras, simplifying the setup, control and acquisition from any number and type of camera.

Proper citation: StreamPix (RRID:SCR_015773) Copy   

•   Source: SciCrunch Registry

http://www.syngene.com/genesys-2/

Imaging software that works with G:BOX Chemi and PXi imaging systems to automatically or manually capture images. GeneSys also includes a database containing information about applications such as fluorescence, chemiluminescence and chemifluorescence.

Proper citation: GeneSys (RRID:SCR_015770) Copy   

•   Source: SciCrunch Registry