Avizo lab: Segment and measure Aspirin pills¶

Date: Jan 22, Jan 27

Dataset: aspirin pill

pdf: AvizoClassI&II.pdf

Work on pills dataset¶

open aspirin pill raw dataset, data range, histogram
visualize: orthoslice, volume rendering, isosurface (rendering)
pre-processing: image filtering
- median filter
- bilateral filter
create binary data:
- segmentation - threshold tool
- interactive threshold + fill holes/closing
separate objects into labels
- image morphology – erosion – does not work well – too much connection
- fast watershed algorithm - separate objects – works but requires extended license
- manual segmentation - threshold - 3D lassol/2D brush to remove connecting voxels
- Advanced: distance map + H-maxima + marker based watershed
- Advanced: distance map + Hierarchial watershed
label individual pills and measure:
- connected components: produce regions (label) dataset, and component spreadsheet
- Labeling, filter by measure
- label analysis and analysis filter – require extended license

clipping plane / slice
generate surface and surface view
Mask by label
compare two orthoslices ( for two different dataset ):
- make sure two orthoslices have the same orientation and slice number
- show/hide one of them to switch between the two
orthoslice with color wash ( compare two dataset ):
- add orthoslice to one dataset
- click triangle from orthoslice, select color wash
- in “data” port of colorwash, choose the second dataset
- choose average weight sum, and change the weight slider