Additional Information

Model classes and types

This table lists all supported model classes and types in this version of CellOrganizer

2D/3D Model Class Model Type Depends on Produces
2D vesicle gmm nuclear_membrane & cell_membrane vesicle
2D nuclear_membrane medial_axis   nuclear_membrane
2D cell_membrane ratio nuclear_membrane cell_membrane
3D vesicle gmm nuclear_membrane & cell_membrane vesicle
3D nuclear_membrane cylindrical_surface   nuclear_membrane
3D cell_membrane ratio nuclear_membrane cell_membrane
2D framework diffeomorphic   cell_membrane, nuclear_membrane
3D framework diffeomorphic   cell_membrane, nuclear_membrane
3D network microtubule_growth nuclear_membrane & cell_membrane microtubule

Reproducing Figures from Research Articles

This table is a guide to specific demos included with CellOrganizer that generate figures similar to those presented in publications that used CellOrganizer to analyze particular datasets. Some demos will generate the same figures as in the research article and others will build a similar output, e.g. same figure different synthetic image.

Article Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10
Johnson et a. (2105)   demo3D27                
Li et al. (2012)   demo3D00, demo3D02   demo3D04 demo3D35          
Buck et al. (2012) demo2D01 demo3D11   demo2D02, demo3D09   demo3D04        
Murphy (2012) demo2D01 demo3D11                
Peng and Murphy (2011) demo3D11             demo3D02    
Shariff et al (2011) demo3D04 demo3D04                
Murphy (2010)       demo3D01   demo2D00        
Shariff et al. (2010) demo3D01, demo3D14     demo3D07, demo3D06   demo3D35 demo3D35 demo3D35    
Peng et al. (2009)   demo2D04, demo3D15, demo3D20     demo3D15