TubeTK/Events/2010.07.26: Difference between revisions
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(Created page with '= Andinet = * Primary goal: Data from Duke for BWH * Accomplishments ** Attend NAMIC AHM ** Determine what is necessary to record data sent to OpenIGTLink from VectorVision syst…') |
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* Primary goal: Bump and dent identification on IC images | * Primary goal: Bump and dent identification on IC images | ||
* Accomplishments | * Accomplishments | ||
** Traveled to SSRL to view the acquisition and meet with Greg and Mike. | |||
** Modified the GenerateFeatures application to handle the input of arbitrary feature images | |||
** Using the previous features and Casey's new patch-based features, was able to achieve 95% pixel level accuracy in Weka and 23/25 defects found with 0 false positives in image space (after morphology). | |||
** Explore new features | ** Explore new features | ||
*** evaluate a variety of standard deviations for intensity and ridge computations | *** evaluate a variety of standard deviations for intensity and ridge computations | ||
* Near Term (Aug 2) | |||
** Receiving code to simulate the tomography directly on GDS Layers | |||
* Near Term (Aug | ** Compute dot-product between line (hessian) tangent and normal directions in ES and GDS images | ||
** | ** Subselect features | ||
** | |||
** Product: ~ 5 slides / report to USC illustrating path chosen, strengths, and weaknesses. | ** Product: ~ 5 slides / report to USC illustrating path chosen, strengths, and weaknesses. | ||
*** Real-world tests / workflow | *** Real-world tests / workflow | ||
| Line 39: | Line 34: | ||
**** i.e., do we need to insert modifications for training on every slice / acquisition / ? | **** i.e., do we need to insert modifications for training on every slice / acquisition / ? | ||
**** Normalizing for inter-acquisition (or inter-slice) variations? | **** Normalizing for inter-acquisition (or inter-slice) variations? | ||
** | ** Work with new collaborator at Kitware. | ||
* Medium term ( | * Medium term (August 15) | ||
** Delivery and education | ** Delivery and education | ||
** Can we get better in simulation? | ** Can we get better in simulation? | ||
Revision as of 16:20, 26 July 2010
Andinet
- Primary goal: Data from Duke for BWH
- Accomplishments
- Attend NAMIC AHM
- Determine what is necessary to record data sent to OpenIGTLink from VectorVision system
- Define data workflow and software architecture
- Begin implementation
- Product: powerpoint presentation: 5 slides
- Near term (August 1)
- Install VV at Duke
- Determine if we can get US data from Duke machine
- Write IJ article
- Cite grant proposal in article
- Medium term (1.5 months, August 15)
- Investigate simulation of ultrasound from MR/CT (Talk to Stephen First :) )
- Code review of vessel segmentation method from Stephen
Patrick
- Primary goal: Bump and dent identification on IC images
- Accomplishments
- Traveled to SSRL to view the acquisition and meet with Greg and Mike.
- Modified the GenerateFeatures application to handle the input of arbitrary feature images
- Using the previous features and Casey's new patch-based features, was able to achieve 95% pixel level accuracy in Weka and 23/25 defects found with 0 false positives in image space (after morphology).
- Explore new features
- evaluate a variety of standard deviations for intensity and ridge computations
- Near Term (Aug 2)
- Receiving code to simulate the tomography directly on GDS Layers
- Compute dot-product between line (hessian) tangent and normal directions in ES and GDS images
- Subselect features
- Product: ~ 5 slides / report to USC illustrating path chosen, strengths, and weaknesses.
- Real-world tests / workflow
- Does a trained classifier work on other layers?
- Does a trained classifier work on other acquisitions?
- i.e., do we need to insert modifications for training on every slice / acquisition / ?
- Normalizing for inter-acquisition (or inter-slice) variations?
- Work with new collaborator at Kitware.
- Medium term (August 15)
- Delivery and education
- Can we get better in simulation?
- Connectivity analysis
Casey
- Primary goal: Compare populations of vascular networks
- Near term (0.5, Aug 1)
- Collaborate with Patrick
- Feature extraction
- Patch-based features (max, median, quantiles)
- Scales / neighborhood
- Feature research
- Width estimate from Stephen (concern, time)
- Location of local max in ridgeness
- Subsample centerlines
- Optimal match filter
- Classifiers
- Comparison
- Implementation for transfer to USC
- Hierarchy (Good/bad. If bad, then add/sub.)
- Feature extraction
- Data for Retinas
- Collaborate with Patrick
- Medium term (1 months, Aug 15)
- Review previous processing pipeline with Stephen
- Research on methods for comparing spatial graphs / adjacency matrices
- Begin Port and test existing adjacency code
- Process retinal data
- Complete port and test of existing adjacency code
- Prepare IJ article
Hua
- Primary goal: ultrasound image processing
- Accomplished
- Verify Andinet's code: add tests and help with IJ publication
- Creating tests (sin pattern with known derivatives)
- Verify Andinet's code: add tests and help with IJ publication
- Near term (August 1)
- Increase coverage of TubeTK
- Update registration code
- Begin investigation of registration metrics that depend on ultrasound probe orientation
- Get data from InnerOptic
- Design phantom or use something from InnerOptic
- Discuss with InnerOptic
- CIRS Phantom
- http://www.insight-journal.org/midas/item/view/2206
- http://www.insight-journal.org/midas/item/view/117
- Get data from InnerOptic
- Medium term (1.5 months
- Investigate use of speckle in ultrasound registration
- Model-based deformation field interpolation
- 2D-3D registration (data)
- Simulating ultrasound from MR/CT
