Understanding living systems
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meshing [2019/05/15 21:45] Igor Chernyavsky [Overview] Links from Martin Turner and Alberto Gambaruto |
meshing [2023/05/04 21:36] (current) Igor Chernyavsky [Overview] - added SuperSegger + Omnipose |
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===== Segmentation and Meshing tools for Image-based Modelling ===== | ===== Segmentation and Meshing tools for Image-based Modelling ===== | ||
- | Credits: Russell Garwood, David Smith, Yongle Sun, Martin Turner (Manchester), Jon Hill (York), Susheel Varma (Sheffield), Gowsihan Poologasundarampillai (Birmingham & DLS), Alberto Gambaruto (Bristol)\\ | + | Credits: Russell Garwood, David Smith, Yongle Sun, Martin Turner (Manchester), Jon Hill (York), Susheel Varma (Sheffield), Gowsihan Poologasundarampillai (Birmingham & DLS), Alberto Gambaruto (Bristol). |
- | //Disclaimer//: The list and descriptions are unavoidably subjective. Please [[question@math-biophys.info|get in touch]] if you notice any inaccuracies. | + | |
+ | <wrap lo>//Disclaimer//: The list and descriptions are unavoidably subjective. Please [[question@math-biophys.info|get in touch]] if you notice any inaccuracies.</wrap> | ||
==== Overview ==== | ==== Overview ==== | ||
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| [[https://diamondlightsource.github.io/SuRVoS|SuRVoS]] | Linux/Win | 0 | Machine learning (ML)-based semi-automatic volume segmentation aimed at X-ray tomography | | | [[https://diamondlightsource.github.io/SuRVoS|SuRVoS]] | Linux/Win | 0 | Machine learning (ML)-based semi-automatic volume segmentation aimed at X-ray tomography | | ||
| [[http://bio3d.colorado.edu/imod|IMOD]] | all | 0 | 3D reconstruction, segmentation and visualisation aimed at Electron Microscopy | | | [[http://bio3d.colorado.edu/imod|IMOD]] | all | 0 | 3D reconstruction, segmentation and visualisation aimed at Electron Microscopy | | ||
- | | [[http://www.itksnap.org|ITK-SNAP]] | all | 0 | User-friendly 3D (semi-)manual segmentation with some ML features for medical MRI, CT and US data | | ||
- | | [[https://www.cti.gov.br/en/invesalius|InVesalius]] | all | 0 | Basic image reconstruction for MRI and (micro)tomography data | | ||
| [[http://mib.helsinki.fi/features.html|Microscopy Image Browser]] | all | 0 | ''Matlab''-based 2D/3D visualisation and segmentation tools for SEM and tomography | | | [[http://mib.helsinki.fi/features.html|Microscopy Image Browser]] | all | 0 | ''Matlab''-based 2D/3D visualisation and segmentation tools for SEM and tomography | | ||
+ | | [[https://hyperspy.org/|HyperSPy]] | all | 0 | ''Python''-based visualisation & analysis of multi-dimensional images & //spectra// (for EM, etc.) | | ||
+ | | [[https://glueviz.org/|GlueViz]] | all | 0 | ''Python''-based visualisation & statistics of //linked// high-dim datasets (astronomy/climate/medical) | | ||
+ | | [[http://www.itksnap.org|ITK-SNAP]] | all | 0 | User-friendly 3D (semi-)manual segmentation with ML features for medical (MRI/CT/US) data | | ||
+ | | [[https://www.cti.gov.br/en/invesalius|InVesalius]] | all | 0 | Basic image reconstruction for MRI and (micro)tomography data | | ||
| [[https://www.slicer.org|3D Slicer]] | all | 0 | Advanced ''VTK''-based 3D visualisation and segmentation of medical images | | | [[https://www.slicer.org|3D Slicer]] | all | 0 | Advanced ''VTK''-based 3D visualisation and segmentation of medical images | | ||
| [[http://www.paraview.org|ParaView]] | all | 0 | ''VTK''-based 3D simulation data visualisation, a free analogue to ''TecPlot'', ''Origin'', ''Igor Pro'', etc. | | | [[http://www.paraview.org|ParaView]] | all | 0 | ''VTK''-based 3D simulation data visualisation, a free analogue to ''TecPlot'', ''Origin'', ''Igor Pro'', etc. | | ||
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| [[http://spiers-software.org|SPIERS]] | Win/Mac | 0 | Tomographic visualisation, serial rendering and meshing (not actively updated since 2013) | | | [[http://spiers-software.org|SPIERS]] | Win/Mac | 0 | Tomographic visualisation, serial rendering and meshing (not actively updated since 2013) | | ||
| [[http://www.sci.utah.edu/cibc-software/seg3d.html|Seg3D]] + ImageVis3D | all | 0 | Visualisation and segmentation of medical images | | | [[http://www.sci.utah.edu/cibc-software/seg3d.html|Seg3D]] + ImageVis3D | all | 0 | Visualisation and segmentation of medical images | | ||
+ | | [[http://mtshasta.phys.washington.edu/website/SuperSegger.php|SuperSegger + Omnipose]] | all | 0 | MATLAB/Python ML-based segmentation & tracking of bacterial cells in 2D microscopy | | ||
+ | | [[https://www.theobjects.com/dragonfly/features.html|Dragonfly]] | Win/Linux | Edu/$$$ | 3D visualisation, CNN-aided segmentation, analysis & meshing [part-limited to ZEISS Pro] | | ||
| FEI [[https://www.fei.com/software/avizo3d|Avizo]] / [[https://www.fei.com/software/amira-3d-for-life-sciences/|Amira]] | all | $$ | Powerful 3D visualisation, image processing and segmentation | | | FEI [[https://www.fei.com/software/avizo3d|Avizo]] / [[https://www.fei.com/software/amira-3d-for-life-sciences/|Amira]] | all | $$ | Powerful 3D visualisation, image processing and segmentation | | ||
| PerkinElmer [[|Columbus]]| all | $$? | Browser-based integrated data storage and basic image analysis system (aimed at pharma) | | | PerkinElmer [[|Columbus]]| all | $$? | Browser-based integrated data storage and basic image analysis system (aimed at pharma) | | ||
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**Tips**: test the final mesh quality by plotting the distribution of //dihedral angles//. See also an overview of meshing tips for ''COMSOL'': [[https://uk.comsol.com/blogs/how-to-set-up-a-mesh-in-comsol-multiphysics-for-cfd-analyses/|Part I]], [[https://uk.comsol.com/blogs/your-guide-to-meshing-techniques-for-efficient-cfd-modeling|Part II]]. | **Tips**: test the final mesh quality by plotting the distribution of //dihedral angles//. See also an overview of meshing tips for ''COMSOL'': [[https://uk.comsol.com/blogs/how-to-set-up-a-mesh-in-comsol-multiphysics-for-cfd-analyses/|Part I]], [[https://uk.comsol.com/blogs/your-guide-to-meshing-techniques-for-efficient-cfd-modeling|Part II]]. | ||
- | **Further Tools and Resources**: [[http://www.ccpi.ac.uk/node/3|Quantification and Segmentation Tools for Micro-Tomography]], [[https://idoimaging.com|Software Catalogue for Medical Imaging]] (e.g. DICOM); [[http://niftyweb.cs.ucl.ac.uk|NiftyWeb]] & [[http://cmictig.cs.ucl.ac.uk/wiki/|Nifty]] (online MRI/CT segementation; [[http://niftynet.io|NiftyNet]] is ML-based); [[https://mirtk.github.io|MIRTK]] and [[http://www.deformetrica.org|Deformetrica]] (MRI-oriented multi-modal image registration and transformation). Meshing tools: [[http://www.meshrepair.org|Mesh Repair Sofware]] (e.g. see ''ReMESH''), [[https://openfoamwiki.net/index.php/SnappyHexMesh|SnappyHexMesh]] from the ''OpenFOAM'' suite. | + | **Further Tools and Resources**: [[http://www.ccpi.ac.uk/node/3|Quantification and Segmentation Tools for Micro-Tomography]], [[https://idoimaging.com|Software Catalogue for Medical Imaging]] (e.g. DICOM); [[http://niftyweb.cs.ucl.ac.uk|NiftyWeb]] & [[http://cmictig.cs.ucl.ac.uk/wiki/|Nifty]] (online MRI/CT segementation; [[http://niftynet.io|NiftyNet]] is ML-based); A comparison of [[https://peterfalkingham.com/2019/02/18/free-software-for-ct-segmentation-2019|CT-segmentation tools]]; [[https://mirtk.github.io|MIRTK]] and [[http://www.deformetrica.org|Deformetrica]] (MRI-oriented multi-modal image registration and transformation). Meshing tools: [[http://www.meshrepair.org|Mesh Repair Sofware]] (e.g. see ''ReMESH''), [[https://openfoamwiki.net/index.php/SnappyHexMesh|SnappyHexMesh]] from the ''OpenFOAM'' suite. |
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