Documentation/Labs/ImageStacks - Revision history

Pieper: /* Options */

2019-10-28T20:31:38Z

Options

Pieper: /* Work in Progress */

2019-10-21T14:22:00Z

Work in Progress

Pieper: /* Work in Progres */

2019-10-17T20:23:12Z

Work in Progres

Pieper: /* Options */

2019-10-16T20:05:07Z

Options

Pieper: /* Options */

2019-10-16T20:03:07Z

Options

Pieper: /* Desired properties */

2019-10-01T17:34:02Z

Desired properties

Pieper: /* Options */

2019-10-01T17:18:41Z

Options

Pieper: Created page with "== Background == Image stacks are generated in a lot of scenarios, like microscopes, microCT, and other non-medical sources. Examples are like:

     directoryPath = '/V..."

2019-10-01T17:17:48Z

Created page with "== Background == Image stacks are generated in a lot of scenarios, like microscopes, microCT, and other non-medical sources. Examples are like: <pre> directoryPath = '/V..."

New page

== Background ==

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

Examples are like:
<pre>
directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'
pathFormat = '%s/1326__rec%04d.png'
</pre>

== Common issues ==
* 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)

== Current reader ==

Delegates to ITK via vtkITKArchetype mechanism. Lots of hidden logic to guess possible mapping from image files to volumes.
* Guesses filename pattern, which can easily fail
* Creates vector volume for RGB and user must manually convert to scalar
* Reads full volume and then must crop or resample
* Can be slow to read / decompress large files

== Available readers ==

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

== Desired properties ==

* 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)

== Options ==

Implementation
* stand-along 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

Features
* store pyramid files in nrrd or some minimal dicom
* option: put dicom files in database for reuse
* option: use low-res as visualization proxy but use fill res for processing

← Older revision		Revision as of 14:22, 21 October 2019
Line 62:		Line 62:

	== Work in Progress ==		== Work in Progress ==
		+
		+	As of October 2019, the repo below has an implementation that works for slice files ready by SimpleITK (png, tiff, etc) extracting one component and options for 50% downsampling.

	* https://github.com/pieper/SlicerImageStacks		* https://github.com/pieper/SlicerImageStacks

@@ Line 61: / Line 61: @@
 * option: use low-res as visualization proxy but use fill res for processing
-== Work in Progres ==
+== Work in Progress ==
 * https://github.com/pieper/SlicerImageStacks

← Older revision		Revision as of 20:03, 16 October 2019
Line 60:		Line 60:
	* option: put dicom files in database for reuse		* option: put dicom files in database for reuse
	* option: use low-res as visualization proxy but use fill res for processing		* option: use low-res as visualization proxy but use fill res for processing
		+
		+	== Work in Progres ==
		+
		+	* https://github.com/pieper/SlicerImageStacks

@@ Line 52: / Line 52: @@
 Implementation
-* stand-along processing script with command line options -- too difficult for users in general, no interactive feedback
+* 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

@@ Line 47: / Line 47: @@
 * allow scripted use outside slicer
 * use reference volume or ROI to define desired geometry (e.g. reuse crop volume logic)
 == Options ==