3D cell tracking using Gaussian Mixture Model (TGMM) |
Software |
|
|
Workflow |
|
Free and open source |
Cell tracking |
Bioimage informatics, Live sample imaging, Light-sheet microscopy |
3D confocal noise simulator |
Software |
|
|
Component |
|
Commercial |
|
|
3D estimation of synaptic vesicle distribution in serial section TEM (ssTEM) |
Software |
|
|
Workflow |
Automated |
I do not know |
|
|
3D Fill holes (mcib3d) |
Software |
|
mcib3d library, ImageJ |
Component |
Automated |
Free and open source |
Morphological operation |
|
3D Generalized Riesz-Wavelet Toolbox for Matlab |
Software |
|
MATLAB |
Component |
Semi-automated |
Free and open source |
Image feature detection |
Bioimage informatics |
3D ImageJ Suite |
Software |
|
ImageJ, ImageScience.jar |
Collection |
Automated, Manual, Semi-automated |
Free and open source |
Colocalisation analysis, Image segmentation, Object feature extraction, Morphological operation, Visualisation |
Bioimage informatics |
3D intensity profile |
Software |
|
Fiji |
Component |
Automated |
Free and open source |
|
|
3D Nuclei Clustering Tool |
Software |
|
ImageJ |
Workflow |
Automated, Semi-automated |
Free and open source |
Clustering |
Fluorescence microscopy |
3D object based colocalisation |
Training Material |
|
|
|
|
|
|
|
3D object based colocalization using KNIME |
Software |
|
KNIME Image Processing and Analysis |
Workflow |
Automated |
I do not know |
Object-based colocalisation, Colocalisation analysis |
|
3D Objects Counter |
Software |
|
Fiji, ImageJ |
Component |
Automated |
Free and open source |
Object feature extraction, Shape features, Object counting |
Fluorescence microscopy |
3D OrthoViewer (Icy) |
Software |
|
|
Component |
Semi-automated |
Free and open source |
Image visualisation |
Bioimage informatics |
3D PSF estimator |
Software |
|
ImageJ, Fiji, MosaicSuite |
Component |
Automated |
Free and open source |
Image feature detection |
Fluorescence microscopy |
3D Segmentation & visualization of nanoparticles attached to the surface of red blood cells |
Software |
|
ImageJ |
Workflow |
Automated |
Free and open source |
Object feature extraction |
Fluorescence microscopy |
3D segmentation (reconstruction) and modeling using Free-D |
Software |
|
|
Workflow |
Automated, Manual, Semi-automated |
Free but not open source |
Image registration, Analysis, Image segmentation |
|
3D Slicer |
Software |
|
3D Viewer, ITK |
Collection |
Automated |
Free and open source |
|
|
3D Surface Plot |
Software |
|
ImageJ |
Component |
Manual |
Free and open source |
Visualisation |
Bioimage informatics |
3D vessel segmentation of synchrotron phase contrast tomography |
Software |
|
Fiji, ilastik |
Workflow |
Semi-automated |
Free but not open source |
Image analysis, Interactive segmentation |
Bioimage informatics, Tomography, Machine learning |
3D Viewer |
Software |
|
ImageJ, 3D Viewer |
Component |
Manual, Semi-automated |
Free and open source |
Visualisation |
Bioimage informatics |
3D-DAOSTORM |
Software |
|
|
Component |
Semi-automated |
Free and open source |
Single molecule localisation |
Super-resolution microscopy, Single molecule localization microscopy |