Tools For Analyzing Large 3D Datasets

This repository is a set of tools for processing and analyzing terabyte size 3D segmentation datasets using Dask. Processing tools involve reading in dataset(s) and outputting another - processed - dataset. These processing tools include the calculation of:

1. Connected Components: includes thresholding and masking
2. Contact Sites: includes setting a distance for contact sites
3. Filling holes: fills holes in segmentations
4. Filtering ids: filters segmented ids to remove unwanted ones.

In addition, there are also tools for analysis of the 3D datasets including:

1. Measurement: measures a variety of properties of the segmented ids (volume, surface area, etc.) as well as properties of contact sites (volume, surface area, contacting objects, etc.).
2. Fitting lines to segmentations: useful for cylindrical-type objects.
3. Assigning to cells: Assigns objects to the cells they are in based on the center of mass lcoations of the cells.

TODO: Include a detailed description of installation and running the code