step-fields

Overview

STEP is a work in progress medical image computing project.

The goal is to implement GPU accelerated volume calculations using JavaScript and WebGL 2.0. Everything should run in the browser with only data access coming from external servers.

Internal data structures should be as close as possible to native DICOM representations.

Conventions

Spaces

Coordinates and matrices are defined with respect to reference coordinates with these names:

Patient or LPS is world space in millimeters with respect to the subject (patient) in LPS convention (left, posterior, superior) as defined in DICOM and Slicer.

Pixel or IJK is index space of the array. Layout in memory is as defined by the DICOM multiframe dataset values, but is for now implemented as pixel = volume[k][j][i] or pixel = volume[slice][row][column] where slice goes from 0 to dataset.NumberOfFrames-1, row goes from 0 to dataset.Rows-1, and column goes from 0 to dataset.Columns-1. The elements of a pixel coordinate are stored in column, row, slice order for consistency with stp space order.

Texture or stp is coordinate access when the volume is loaded in a WebGL 3D texture. Here the coordinates are 0 to 1 with sample.s selecting the column, sample.t selecting the row, and sample.p selecting the slice (reverse order of Pixel space).

Naming

Values that map from one space to another are named to indicate the direction of mapping. E.g. patientToPixel is a 4x4 matrix that maps from LPS space to slice,row,colum space and textureToPixel is a vec3 that goes from stp space to slice,row,colum.

Acknowledgments

This work is supported in part by the Neuroimage Analysis Center, 4P41EB015902.