New Release! CellOrganizer v2.7.1 and CellOrganizer for Docker

CellOrganizer Version 2.7.1

The latest release of CellOrganizer now includes methods to generate reports from generative models. slml2info replaces model2info, and creates a report with useful information from a single generative model file. slml2report creates a report comparing two generative model files. Both methods write reports with Matlab Publisher, and when deployed as binaries, they generate a report in Markdown using pandoc.

In the previous version of CellOrganizer (2.7.0), a Principal Components Analysis (PCA) model for 2D cell/nuclear shapes was implemented. The PCA model takes less time to train and performs better at shape reconstruction than the diffeomorphic framework model. In CellOrganizer 2.7.1, we’ve created demos demo2D08 and demo2D09 to show how to build reports from a PCA framework model.

CellOrganizer for Docker!

With CellOrganizer for Docker, users who do not have access to a Matlab license can run the main tools from CellOrganizer! Using Docker, software installations are compatible across most operating systems, including Ubuntu, MacOSX and Windows. The Docker container has the four binaries corresponding to the main tools as well as a collections of scripts to help you get started training generative models, synthesizing images and generating reports.