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http://www.meshmixer.com

3D visualization software for working with triangle meshes. This software also can clean up 3D scans, design objects for 3D printing, and perform other 3D design-related functions.

Proper citation: Autodesk Meshmixer (RRID:SCR_015736) Copy   

•   Source: SciCrunch Registry

http://remesh.sourceforge.net/

3D editing software for manifold triangle meshes with advanced repairing features. It can post-process polygon meshes coming from digitization sessions and automatically filter out most of the typical flaws that models may have when coming from a 3D digitization session (degenerate triangles, isolated vertices, noise, topological artefacts, holes, ...).

Proper citation: ReMESH (RRID:SCR_015735) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimerax/

Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.

Proper citation: UCSF ChimeraX (RRID:SCR_015872) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/users/crisco/jiv/

JIV is a Java software for visualization and side-by-side comparison of multiple 3D image datasets. While it was originally designed for remote data access, it can be used as a traditional local application as well. It features include being highly portable and platform-independent, the ability to run with a common Web browser and to cope with slow network links, an independent 3D image data format, and a display of gray-level (intensity) image data with a user-controlled color-mapping, among other features.

Proper citation: JIV: A 3D Image Data Visualization and Comparison Tool (RRID:SCR_008657) Copy   

•   Source: SciCrunch Registry

http://www.cyto.purdue.edu/cdroms/micro1/7_spon/vaytek/voxblast.htm

Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.

Proper citation: VoxBlast (RRID:SCR_016491) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/HARP

Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.

Proper citation: HARP (RRID:SCR_016546) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/vpv

Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.

Proper citation: VPV (RRID:SCR_016545) Copy   

•   Source: SciCrunch Registry

https://github.com/g2-bernotas/PS-Plant-Framework

Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters.

Proper citation: PS-Plant Framework (RRID:SCR_017032) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neuroinfo

Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies.

Proper citation: NeuroInfo (RRID:SCR_017346) Copy   

•   Source: SciCrunch Registry

https://github.com/padster/pyDynamo/

Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.

Proper citation: Dynamo (RRID:SCR_017541) Copy   

•   Source: SciCrunch Registry

http://xray.bmc.uu.se/~alwyn/TAJ/Home.html

Software for visualization of macromolecular structures, atomic coordinates, and 3D intensity maps, and for building macromolecular structures.

Proper citation: O (RRID:SCR_018394) Copy   

•   Source: SciCrunch Registry

https://www.repetier.com/

Open source 3D printing software which supports multi part printing and has slicers.

Proper citation: Repetier Host (RRID:SCR_018901) Copy   

•   Source: SciCrunch Registry

https://www.siemens-healthineers.com/en-us/angio/options-and-upgrades/clinical-software-applications/syngo-dynact

Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging.

Proper citation: syngo DynaCT (RRID:SCR_018902) Copy   

•   Source: SciCrunch Registry

https://www.cmiss.org/cmgui

Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs.

Proper citation: CMGUI (RRID:SCR_019271) Copy   

•   Source: SciCrunch Registry

https://www.panda3d.org/

Open source game engine and framework for 3D rendering and game development for Python and C++ programs. Graphics engine and programming environment to support everything from real time graphics applications to development of high end virtual reality theme park attractions or video games.

Proper citation: Panda3D (RRID:SCR_021216) Copy   

•   Source: SciCrunch Registry

https://github.com/spoonsso/dannce

Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking.

Proper citation: DANNCE (RRID:SCR_023061) Copy   

•   Source: SciCrunch Registry

https://github.com/lucadellasantina/ObjectFinder

Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes.

Proper citation: ObjectFinder (RRID:SCR_023319) Copy   

•   Source: SciCrunch Registry

https://github.com/JenHungWang/ECTI_Atopic_Dermatitis/blob/master/README.md

Software repository presents objective, quantifiable method for assessing severity of atopic dermatitis.

Proper citation: ECTI_Atopic_Dermatitis (RRID:SCR_025706) Copy   

•   Source: SciCrunch Registry

https://webknossos.org

Web tool for 3D data annotation for connectomics.Open source tool for annotating and exploring large 3D image datasets. Web based data sharing, annotation and visualization software for large scale 3D images. Provides flight mode, single view egocentric reconstruction method enabling to reconstruct for axons and for dendrites in 3D electron microscopic data from mammalian cortex. Supports skeleton and volumetric annotations as well as data management functionality.

Proper citation: webKnossos (RRID:SCR_020979) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=TrumpetPlots

Software R package to visualize relationship between allele frequency and effect size in genetic association studies.

Proper citation: TrumpetPlots (RRID:SCR_023742) Copy   

•   Source: SciCrunch Registry