deep learning of tissue specific speckle representations in optical coherence tomography and deeper...
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Deep Learning of Tissue Specific Speckle
Representations in Optical Coherence
Tomography and Deeper Exploration for
In situ Histology
Debdoot Sheet
@ Department of Electrical Engineering, Indian Institute of Technology Kharagpur, India.
Sri Phani Krishna Karri, Jyotirmoy Chatterjee
@ School of Medical Science and Technology, Indian Institute of Technology Kharagpur, India
Amin Katouzian, Nassir Navab
@ Chair for Computer Aided Medical Procedures, TU Munich, Germany
Ajoy K. Ray
@ Electronics and Electrical Comm. Engg., Indian Institute of Technology Kharagpur, India.
1ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet
Motivation• Soft tissues – e.g. skin
– Epithelial
– Connective
– Muscular
– Adipose
• Pathological markers– Extracellular matrix deposition
– Cellular atypia and dysplasia
– Loss of histo-architecture
– Proliferative changes
• Conventional histology– Patient discomfort
– 48-72 hours delay in processing
• Alternatives – Subsurface imaging
• Optical coherence tomography (OCT)
• Challenges with the alternative– Hard to interpret
– Stochastic uncertainty of speckles
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 2
Epithelium, Papillary
dermis, Dermis, Adipose
Where do we stand now?
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 3
This Paper
Text books
R. K. Das (2012), PhD Thesis
A. Barui (2011), PhD Thesis
D. Sheet et.al., ISBI 2014
State of the Art• In situ Histology with OCT
– G. van Soest et al., (2010), G. J. Ughi et al., (2013) –Cardiovascular OCT
– D. Sheet et al., (2013, 2014) –Cutaneous wounds, oral
• Challenges– Heuristic features
• Texture
• Intensity statistics
– Heuristic computational models• Transfer learning of speckle
occurrence models
– Incomplete representation dictionary
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 4
Multi-scale
modeling of
OCT speckles
Training
image
set Ground
truth
Random forest
learning
Multi-scale
modeling of
OCT speckles
Test image
Labeled
tissue
Heuristics in State of Art
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 5
The Solution
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 6
Den
oisi
ngA
uto
Enc
oder
Den
oisi
ngA
uto
Enc
oder
Logi
stic
Reg
.
Unfurling the Deep Network
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 7
Learning of Representations
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 8
Representation of speckle
appearance models learned by DAE1
Learning of Representations
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 9
Sparsity of representations learned by
DAE2
Experiment Design• Data Collection
– School of Medical Science and Technology, Indian Institute of Technology Kharagpur
– 1300 nm (HPBW 100 nm) Swept Source OCT System • OCS 1300 SS, ThorLabs, NJ,
USA
• 8 bit bitmap images
– Histology for ground truth• HE stained
• Samples– Mus musculus (small mice)
– 16 healthy skin
– 2 wounds on skin
• DNN architecture– Patch size – 36 × 36 px
– DAE1 – 400 nodes
– DAE2 – 100 nodes
– Target – Logistic Reg. • 5 outputs
– Sparsity – 20%
– Mini-batch training
• In situ Histology Performance– Epithelium – 96%
– Papillary dermis – 93%
– Dermis – 99%
– Adipose tissue – 98%
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 10
Results in Wounds
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 11
(a) OCT image of wound (b) Ground truth (c) In situ histology
Epithelium, Papillary
dermis, Dermis, Adipose
Epithelium, Papillary
dermis, Dermis, Adipose
Take Home Message• Photons interact characteristically with different tissues.
– Stochastic similarity exists in speckle appearance.
– Such representations are hard to heuristically encode.
• Deep learning and auto-encoders for computational imaging– Speckle imaging application viz. OCT tissue characterization
– Hierarchical learning• Locally embedded representations.
• Sparsity is in learned (auto-encoded) representations.
ISBI 2015 / FrDT3.5 - Deep Learning of Tissue Specific Speckle... - Debdoot Sheet 12
Queries: Debdoot Sheet (debdoot@ee.iitkgp.ernet.in)
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