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Segmentation TrainerA Robust and User-friendly Machine Learning Image Segmentation Solution
Presented by Mike Marsh, Ph.D.Dragonfly Product Manager
Thursday, March 2, 201710th FIB-SEM Users’ Group MeetingGaithersburg, MD
About ORS▸ Headquartered in Montreal, Canada.▸ Founded in 2004.▸ Registered users in 80 countries.▸ Practicing ISO and IEC standards compliant processes
Visual SI ORS Visual
About ORS▸ Headquartered in Montreal, Canada.▸ Founded in 2004.▸ Registered users in 80 countries.▸ Practicing ISO and IEC standards compliant processes
Dragonfly ORS Visual
Rapid InnovationV2.0 launched September 2016V2.1 coming in April 2017▸ macro engine▸ superpixel segmentation▸ machine learning
segmentation engine▸ In-application store
V2.2 coming in fall 2017(coming to Linux)
TechnologyAnaconda Python 3.5 for scientific computingState-of-the-art image segmentationHigh-impact rendering engine
Extensibility and CommunitySockets for extensions:▸ Embedded online console▸ Object analysis
measurements▸ Image filters▸ Menu-actions▸ Macros▸ Machine Learning classifiers▸ (and more)
App store for sharing and versioning
LicensingFlexible licensing options for various institutional needsFree licensing for non-commercial use in most countries
About Dragonfly
Image SegmentationThe hard way and the easy wayPainstaking:▸ Painting▸ Constrained Painting
▹ Threshold-gated painting▹ Superpixel-bloc painting
Easy, but never good enough:▸ Point-and-click▸ Thresholding (interactive)▸ Thresholding (algorithmically, eg. Otsu’s method)▸ Other tools▸ Automated?
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
Black box classifier segmentation
Input image
Class 1Class 2
Segmentation
Classifier
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
Black box classifier segmentation
FIB-SEM of fuel cell Segmentation
ElectrolyteElectrode
Pore spaceClassifier
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
Black box classifier segmentation
FIB-SEM of fuel cell Segmentation
ElectrolyteElectrode
Pore space
Filter Banks
Use any of the filters in the Image Processing toolbox▸ Smoothing▸ Edge Enhancement▸ Texture
▹ Gabor▹ HoG▹ DoG▹ Standard deviation
Aggregate into filter banks
Pixel classificationSmartGrid cell classification:▸ Superpixel▸ Watershed on Grid▸ Superixel (Scikit-learn)▸ Watershed on Grid (Scikit-learn)
Spatial Discretization
Machine Learning Core
▸ Random Forest▸ Extra-Trees▸ Adaboost▸ Gradient Boosting▸ Bagging▸ K-Nearest Neighbors
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
Black box classifier segmentation
FIB-SEM of fuel cell Segmentation
ElectrolyteElectrode
Pore space
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
Black box classifier segmentation
ElectrolyteElectrode
Segmentation
Pore space
SE
BSE
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
Black box classifier segmentation
ElectrolyteElectrode
Segmentation
Pore space
SE
BSE
Machine learning coreEngineParameters
Spatial discretization settingsSmart Grid (Region) engineParameters
Filter bank (Feature Presets)
Train it
Classifier
ElectrolyteElectrode
Pore space
ElectrolyteElectrode
Segmentation
Pore space
SEimage
BSEimage
Machine learning coreEngineParameters
Spatial discretization settingsSmart Grid (Region) engineParameters
Filter bank (Feature Presets)
Apply it
Classifier ElectrolyteElectrode
Segmentation
Pore space
SEimage
BSEimage
Machine learning coreEngineParameters
Spatial discretization settingsSmart Grid (Region) engineParameters
Filter bank (Feature Presets)
Apply it
Classifier
Mask
ElectrolyteElectrode
Segmentation
Pore space
SEimage
BSEimage
ClassifierMachine learning core
● Engine● Parameters
Spatial DiscretizationSmart Grid (Region)
● Engine● Parameters
Signal TexturesFilter bank (Feature Presets)
It’s modular
ElectrolyteElectrode
Segmentation
Pore space
SEimage
BSEimage
ClassifierDeep Learning core
● Engine● Parameters
Spatial DiscretizationNot necessary
Signal TexturesNot necessary
It’s modular (Deep Learning CNN) Late 2017
ElectrolyteElectrode
Segmentation
Pore space
SEimage
BSEimage
Encourage re-use of Classifiers
▸ Share classifiers with the community in the App Store (Infinite Toolbox) April 2017
▸ Preview classifiers onlineLate 2017
Workflow for Using Classifiers
Build the classifierTrain itTune it▸ Iterate:
▹ Update training classes▹ Tweak engine parameters▹ Add / remove filter banks
review coefficients▹ Retrain
▸ PreviewRe-use it