Ähnlich wie Deep Hierarchical Profiling & Pattern Discovery: Application to Whole Brain Rat Slices After Traumatic Brain Injury - by Jahandar Jahanipour
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THE ROLE OF PHARMACOGNOSY IN TRADITIONAL AND MODERN SYSTEM OF MEDICINE.pptx
Deep Hierarchical Profiling & Pattern Discovery: Application to Whole Brain Rat Slices After Traumatic Brain Injury - by Jahandar Jahanipour
1. Jahandar Jahanipour
Department of Electrical and Computer
Engineering
University of Houston, TX
Deep Hierarchical Profiling & Pattern Discovery:
Application to Whole Brain Rat Slices After Traumatic
Brain Injury
Advisor:
Prof. Badrinath Roysam
2. Introduction
Concussion: disruption in the normal
function of the brain caused by a bump,
blow, …
Headache
Dizziness
Depression
Chris
Henry
John Grimsley
2
1.5 atm Fluid percussion injury multiplexed imaging technique Whole brain rat slice
~ 300,000 cells
~ 3Gb
~32,000 ×47,000 pixels
Motivation: Computational data-driven image interpretation on large datasets
GOAL:
Profile tissue alterations in a manner that
is comprehensive , quantitative and
sensitive to multiple types of changes.
3. Deep Feature Extraction
Nuclear morphological features
are not able to capture
thorough molecular signature.
Associative features are
dependent on nuclear
segmentation of object.
3
NeuN+
NeuN-
40µm
NeuN
DAPI+Histones
Conventional Cytometric Features:
Deep Features:
Nuclear segmentation of cells using DAPI +Histone channels.
Scattering network formed by wavelet-modulus
cascading.
Deep features capture
basal cell morphology and
molecular distribution,
JOINTLY.
4. Can We Perform Computationally Guided
Biological Interpretation?
Can we profile heterogeneity among cells?
4
S100 GFAP
200 µm
20µm
20µm
20µm
Is there any relation between activation level of a cell to the location of the
cell from the center of the injury?
6. Profiling Heterogeneity Within Same Structure
6
Astrocyte
Classification
Biomarkers for astrocyte phenotyping
S100 GFAP GLAST
Resting Astrocytes All (+) Subset (low) Subset (+)
Reactive Astrocytes All (+) All (high) All (+)
S100 GFAP
200 µm
S100-
S100+
S100+
S100-
All cells
Classifying astrocytes
within cortex
Astrocyte can be reconstructed using S100 and GFAP biomarkers for further analysis.
Li+VPa (treatment)
7. Profiling Cell Status Activation
7
S100 GFAP
200 µm
20µm 20µm20µm
S100+S100-
All cells
reactive resting
highmoderate
Astrocyte
Classification
Biomarkers for astrocyte
phenotyping
S100 GFAP GLAST
Resting Astrocytes All (+)
Subset
(low)
Subset (+)
Reactive
Astrocytes
All (+) All (high) All (+)
Moderately active
astrocytes
Very active
astrocytes
Profiling of astrocytes’ activation status reveals the relation of each
cell’s location relative to the site of injury.
Distance to the injury activation
Li+VPa (treatment)
8. Profiling Heterogeneity Within Same Structure
8
200 µm
group 1
group 2
group 3
group 4
group 5
Oligo-glial markers
S100 APC MBP PLP
Laminar-like pattern
resembling cortical
neuronal layers using
oligo-glial biomarkers:
Identifying 5
different cell
subpopulations
organized in
cortical layer
fashion
Profiling of oligo-glial biomarkers to discriminate cortical layers.
LiVPa