Differences

This shows you the differences between two versions of the page.

Link to this comparison view

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
Line 1: Line 1:
 ===== 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 ====
  
Line 9: Line 10:
 | [[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. |
Line 18: Line 21:
 | [[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) |
Line 46: Line 51:
 **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.
  
 \\ \\
meshing.1557956716.txt.gz · Last modified: 2019/05/15 21:45 by Igor Chernyavsky
Recent changes RSS feed
CC Attribution 3.0 Unported
Driven by DokuWiki Valid XHTML 1.0