Documentation/Labs/ImageStacks

Background

Image stacks are generated in a lot of scenarios, like microscopes, microCT, and other non-medical sources.

Examples are like:

    directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'
    pathFormat = '%s/1326__rec%04d.png'

Data is really grayscale, but encoded using jpg or other color format
Data may be large and needs to be cropped or resampled for use
Data will not have any consistent metadata
- pixel / slice spacing
- orientation (e.g. mapping to anatomical coordinates)
- acquisition time, equipment, operator, etc
Only a subset of data may actually be wanted (ROI or subsampled volume)

Delegates to ITK via vtkITKArchetype mechanism. Lots of hidden logic to guess possible mapping from image files to volumes.

vtkPNGReader
itk image IO
Qt Image
PIL / PILLOW python packages (not currently bundled in Slicer, but pip installable)
QWebEngine

fast, ideally multithreaded
compatible with multiple file formats (at least jpg, tiff, bmp, png)
clean slicer integration
support arbitrary file naming conventions with different ways of mapping names to volumes or other structures
ability to map anatomical coordinates (e.g. click on nose, right ear, and top of head)
ability to convert to scalar and/or crop/resample while reading
store pyramid encoded volumes for later reuse
use a single-file format for simplicity (avoid creating even more single slice image files)
store metadata for later reuse
allow scripted use outside slicer
use reference volume or ROI to define desired geometry (e.g. reuse crop volume logic)
handle greater than 8 bits per pixel if the source format supports it

Implementation

stand-alone processing script with command line options -- too difficult for users in general, no interactive feedback
plugin for Add Data module that exposes some options -- not enough room for gui, not interactive
Independent importer module -- probably the best option with reusable logic

Features