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meshing [2017/08/17 18:03]
Igor Chernyavsky Amira tips
meshing [2018/09/13 19:03] (current)
Igor Chernyavsky [Overview]
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 ===== Segmentation and Meshing tools for Image-based Modelling ===== ===== Segmentation and Meshing tools for Image-based Modelling =====
  
-Credits: Russell Garwood, Yongle Sun (Manchester), Jon Hill (York), Susheel Varma (Sheffield)+Credits: Russell Garwood, David Smith, Yongle Sun (Manchester), Jon Hill (York), Susheel Varma (Sheffield), Gowsihan Poologasundarampillai (Birmingham & DLS)
  
 ==== Overview ==== ==== Overview ====
  
 ^ Visualisation & segmentation          ^ Platform  ^ Cost  ^ Comment  ^ ^ Visualisation & segmentation          ^ Platform  ^ Cost  ^ Comment  ^
-| [[http://fiji.sc|FUJI]] / ImageJ + [[http://3dviewer.neurofly.de|3D Viewer]]    | all | 0 | Highly flexible image processing, with limited 3D rendering and meshing |+| [[http://fiji.sc|FIJI]] / ImageJ + [[http://3dviewer.neurofly.de|3D Viewer]]    | all | 0 | Highly flexible image processing, with limited 3D rendering and meshing 
 +| [[https://diamondlightsource.github.io/SuRVoS|SuRVoS]]                    | Linux/Win | 0 | Machine learning-based semi-automatic volume segmentation aimed at X-ray 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://www.slicer.org|3D Slicer]]  | all        | 0    | ''VTK''-based 3D visualisation and segmentation of medical images | | [[https://www.slicer.org|3D Slicer]]  | all        | 0    | ''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. |
 | [[https://www.blender.org|Blender]]   | all        | 0    | Free alternative to ''3D Studio'' / ''Autodesk Maja'' with some mesh manipulation | | [[https://www.blender.org|Blender]]   | all        | 0    | Free alternative to ''3D Studio'' / ''Autodesk Maja'' with some mesh manipulation |
 | [[https://sf.anu.edu.au/Vizlab/drishti|Drishti]] | Win/Mac | 0 | Advanced visualisation and rendering for presentations & outreach; basic meshing | | [[https://sf.anu.edu.au/Vizlab/drishti|Drishti]] | Win/Mac | 0 | Advanced visualisation and rendering for presentations & outreach; basic meshing |
-| [[http://spiers-software.org|SPIERS]] | Win/Mac   | 0     | Tomographic visualisation, serial rendering and meshing                          |+| [[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 |
 | 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) |
 | [[http://www.osirix-viewer.com|OsiriX]]| Mac only  | $    | DICOM data visualisation, FDA-certified for diagnostics | | [[http://www.osirix-viewer.com|OsiriX]]| Mac only  | $    | DICOM data visualisation, FDA-certified for diagnostics |
  
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 **Summary**: ''MeshLab'', ''Gmsh'', ''Simpleware'' are good %%GUI%% tools for simple-to-medium mesh-generation; for high-throughput tasks, use script-based ''Gmsh'', ''Netgen'', ''TetGen'', ''CGAL'', ''iso2mesh'' (all are highly flexible), and also ''ANSYS ICEM''.  **Summary**: ''MeshLab'', ''Gmsh'', ''Simpleware'' are good %%GUI%% tools for simple-to-medium mesh-generation; for high-throughput tasks, use script-based ''Gmsh'', ''Netgen'', ''TetGen'', ''CGAL'', ''iso2mesh'' (all are highly flexible), and also ''ANSYS ICEM''. 
  
-**Tip**: test the final mesh quality by plotting the distribution of //dihedral angles//.+**Tip**: 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]].
  
  
 \\ \\
-==== Amira / Avizo Tips ====+==== ImageJ/Fiji & Amira/Avizo Tips ====
  
-Credits: Kathy Tinoco, Cornelia Vacar (FEI), Philip Pearce (MIT), Alexander Erlich and Sebastian Gilbert (Manchester)+Credits: Kathy Tinoco, Cornelia Vacar (FEI), Philip Pearce (MIT), James Carr, Alexander ErlichSebastian Gilbert and David Smith (Manchester)
  
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 <div rightalign>--- //Igor Chernyavsky, 2017/08/17 17:47// ---</div> <div rightalign>--- //Igor Chernyavsky, 2017/08/17 17:47// ---</div>
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 +**Segmentation Tips** for complex / noisy data:
 +  - ''[[http://imagej.net/Trainable_Weka_Segmentation|Weka]]'' is a 2D/3D machine-learning ''Fiji'' plugin, useful for pre-processing
 +  - //Filter Sandbox// and //Marker-based Watershed Mask// are semi-automatic segmentation modules in ''[[https://en.wikipedia.org/wiki/Amira_(software)|Amira]]''
 +  - ''[[https://diamondlightsource.github.io/SuRVoS/|SuRVoS]]'' is a powerful combination of 3D super-voxel segmentation and trainable classifiers (random forest, etc.)
 +  - ''[[http://mib.helsinki.fi/features_all.html|MIB]]'' is another tool for 2D super-pixel segmentation and has some machine learning functionality (X-ray ZEISS ''.txm'' needs to be exported to ''.mrc''/''.tiff'' stacks first)
 +
 +<div rightalign>--- //Igor Chernyavsky, 2017/09/18 19:00// ---</div>
  
  
meshing.1502989431.txt.gz · Last modified: 2017/08/17 18:03 by Igor Chernyavsky
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