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How to perform : «Objects density (heat-map) and object distribution gradient plotting (profile)»

The application-note purpose is to guide the user in performing the Objects density distribution analysis per volume unit (heat-map).

The same workflow can be used to evaluate the Objects count' distribution gradient along a specific direction (gradient profile). The application uses a Python script to create the contiguous sub-regions (sampling volume) and a pipeline to count the objects and to compute its density per volume unit (single sub-region) or the distribution along the longest direction of the sub-regions structure.

The evaluated Objects can be any biological structures like Cells, Nuclei, Neurons, as well as any small structures like Vesicles, Protein clusters, Mitochondria, and etcetera. The sampling volume can describe and limiting any anatomical regions inside the sample.

The unique limits is related to the sampling volume shape, only regular 3D boxes are available.

Download Full "Application Note #1" PDF

Download "Free-Oriented Sub-volume" Python Script