CellOrganizer v2.9.3

Significant additions have been made to the function (slml2report.m) for comparing two CellOrganizer spharm-obj models of organelle shape and spatial distribution. The report now includes
- improved plots of the spatial distributions of objects, and
- a statistical comparison between the positions of objects (relative to cell and nuclear boundaries) in the two models. This is done by forming a graph of the positions of all objects in both models, finding cliques within that graph, and measuring the fraction of objects from each model in each clique. This is used to calculate the KL divergences between two random halves of the objects in each model (to establish a baseline measure for the single models), and between the four cross-model combinations of halves. The higher the divergences of the cross-model pairs are compared to the within-model pairs, the more different the spatial distributions of the models are considered to be.
The execution time of the SPHARM-RPDM code for constructing cell, nucleus and organelle shape models has been improved through more efficient code for parts of the shape parameterization step contributed by Khaled Khairy (khaled.khairy@stjude.org). Khaled is the Director of the Center for Bioimage Informatics at St. Jude Children’s Research Hospital in Memphis. We gratefully acknowledge his contribution. (EqualAreaParametricMeshNewtonMethod.m, calc_area_jacobian_sphere_KK.m)

Improve object detection for spharm_obj models. (find_objects_local.m, find_objects_local.m, spharm_obj_model.m, spharm_obj_percell_3D.m)

Github Repository

CellOrganizer releases for the 2.0 family are continuously tested using a set of

- - public tests using the Matlab Unit Testing Framework
  - private tests for compatibility with old releases of Matlab

CellOrganizer releases for the 2.8+ family have been tested on