ECSE6963, BMED 6961 Cell

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ECSE-6963, BMED 6961Cell Tissue Image Analysis

• Lecture 16 Feature Selection Validation
• Badri Roysam
• Rensselaer Polytechnic Institute, Troy, New York
  12180.

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Recap Blob Segmentation
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Recap Four Ideas for Blob Segmentation

• Indeed, there are lots of ideas out there!
• Idea 1
• Use other algorithms instead of watershed (e.g.,
  clustering)
• Idea 2
• Touching cells have a membrane between them. If
  the membrane is labeled fluorescently, we have an
  additional cue.
• Idea 3
• Touching cells often exhibit some edges. The
  watershed algorithm does not exploit them.
• Idea 4
• If the touching cells have shapes that can be
  modeled, we can exploit that information to
  improve object separation

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Recap Features of Connected Components

• Area
• Feret box, and minimum enclosing rectangle
• Diameter
• Centroid
• Convexity
• Radius Circularity
• Shape complexity
• Boundary curvature and special points

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Recap

• Combining Ideas
• When we encounter a new application, a
  combination of these ideas can be used
• For highest performance, object modeling is
  essential
• Todays discussion
• This topic continues to evolve
• Of course, new ideas and novel combinations of
  old ones continue to emerge
• E.g., use multiple object models to handle
  diversity of cell types
• Today
• Good and bad features of objects
• Performance Evaluation Validation

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The Feature Selection Problem

• The features that we have studied are only a
  subset of the many that can be defined
• Its fun to invent new features, but theres a
  caveat to consider
• If we consider too many features
• High-dimensional space,
• need too many examples to estimate model
  parameters
• How much accuracy do we really need?
• The curse of dimensionality
• They may not have enough additional
  discriminatory value
• Computationally Expensive

Covers Inequality
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Example Cervical Smears
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Features of Nuclei in Cervical Smears
Absorption Features
Clump
OD
Energy
Energy
mean
1
2
I
I
Corr
Corr
mea
mean
1
2
OD
var
I
Homog
Homog
norm
2
1
R
I
OD
Entropy
Entropy
max
var
int
1
2
R
Contrast
Contrast
mean
2
1
Area
Bclump
CHomog
Elong
Size Features
Fit
R
var
Texture Features
Tort
Shape Features
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Good Features

• A good feature
• Is significantly different for each class
• Has a small variance/spread within each class
• Maximize the Fisher Discriminant ratio
• Is not correlated with another feature in use
• Correlated features are redundant, and increase
  dimensionality without adding value

Bad
Good
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Discriminating Ability

• We start by examining the discriminating power of
  each feature independently
• Qualitative Method
• Clear separation of classes on a scatter plot or
  histogram
• Quantitative Method
• Start with a LABELED scatter plot
• Define two hypotheses
• H0 The values of the feature do not differ
  significantly
• (Null hypothesis)
• H1 The values of the features differ
  significantly
• (Alternative hypothesis)
• The term significantly is quantified by a
  significance level ?.

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Gaussian Basics
If we gather up enough numbers together, their
average will tend to be Gaussian distributed.
Falls Rapidly 95 of the samples fall within two
standard deviations!
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Probabilities Tables
Normalization
To calculate probability that x is in a certain
interval, we need to integrate the Gaussian.
Needed Frequently in statistics. Normalize, and
lookup a table of integrals for N(0,1). Boils
down to
Significance level
Acceptance Interval
Old fashioned Table
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The Sample Mean Variance are Random Variables
Suppose that they are Gaussian distributed, and
mutually independent
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Hypothesis Testing
Suppose that we have just two classes for now.
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Hypothesis Testing
test statistic
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Significance
Suppose we choose a 95 significance level, then
acceptance interval is
If q falls in the above range, decide H0, else
decide H1
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Case when variances are unknown
?
We can no longer use the Gaussian table Need to
use the T-distribution table instead. Needs two
numbers to look up
DOF
Equal/unequal variance
In MATLAB, H ttest2(x,y,alpha, tail, vartype)
Significance (typ. 5)
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Discriminant Functions

• A function of the features that allows us to
  discriminate between classes
• Generalization of the likelihood ratios and
  thresholds

Linear Discriminant

-
Sign of the discriminant tells us the decision
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The Next Step

• The features that pass the individual
  hypothesis tests could still have correlations
  among themselves
• Correlation implies redundancy, and wasted
  dimensions
• Procedure
• Pick the single best feature
• Try all remaining chosen features one at a time,
  and add the one that gives the best improvement
• Repeat until
• The last added feature does not add enough
  improvement to justify an extra dimension

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Stepwise Discriminant Analysis

• We can come up with a selection method that goes
  the other way
• Start off with all features
• Remove one feature at a time
• Continue until performance is still acceptable
• Stepwise discriminant analysis is a method that
  combined top-down and bottom-up approaches
• Generally, not worth writing our own code
• Better to use commercial packages
• The above approaches are still sub-optimal
• THE VERY BEST approach is to exhaustively
  consider all subsets of features and pick the
  best one.
• This is very expensive. For example,

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How do we Test our Model?
Why bother?? Because our model should hold up
over images that we havent processed yet!
Image Selected for Feature Computation and
Labeling
Image to be processed automatically
Select a subset of features, build a discriminant
based on them, and evaluate its effectiveness
over the remaining features
A Batch of Images
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Features of Nuclei in Cervical Smears
Absorption Features
Clump
OD
Energy
Energy
mean
1
2
I
I
Corr
Corr
mea
mean
1
2
OD
var
I
Homog
Homog
norm
2
1
R
I
OD
Entropy
Entropy
max
var
int
1
2
R
Contrast
Contrast
mean
2
1
Area
Bclump
CHomog
Elong
Size Features
Fit
R
var
Texture Features
Tort
Shape Features
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Feature Sets Compared
Nearest
Wiener Filter
Neighbor
Deblurred
Raw Data
Deblurred
Data
Data
2-D
Features
3-D
Features
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Classification Results withLinear Discriminant
Classifier
86
3-D
2-D
Wiener
Wiener
85
Filter
Filter
84
3-D
Nearest
Neighbor
83
3-D
2-D
Nearest
Percent Correct
82
Neighbor
2-D
81
80
79
78
Features Used
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Stepwise Linear Discriminant Analysis Results
Rank
2-D
2-D
2-D
3-D
3-D Nearest
3-D Wiener
Nearest
Wiener
Neighbor
Neighbor
1
R
R
I
R
R
I
mean
mean
norm
mean
mean
norm
2
Corr
Corr
OD
Corr
Corr
OD
2
2
var
2
2
int
3
Clump
Clump
R
Homog
CHomog
OD
mean
1
mean
4
CHomog
Homog
Entropy
CHomog
Clump
CHomog
2
1
Moral Relative importance of features can be
affected by pre-processing
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Validation and Performance Assessment

• Validation
• Is the software systems output valid?
• Essential to adoption by biologist/clinician
• Performance Assessment
• Exactly how well is the software working?
• Surprisingly tricky issue given the subjectivity
  and variability of people
• Inter-subject variability
• Intra-subject variability

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Testing Against a Consensus

• Ask multiple human observers to manually analyze
  the image
• From scratch, or
• By editing the machine output
• Convene a meeting of the human observers
• Discuss differences of opinion on each cell
• Develop a single consensus opinion
• This becomes the Gold Standard
• Compare the software output against the gold
  standard, and measure concordance

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Classical Multiple-Observer Validation
Manual Segmentation by observer 1
Manual Segmentation by observer 2
Image
Consensus Building
Measure(s) of automated segmentation performance
Quantitative Comparison
Manual Segmentation by observer N
Automated Segmentation
Appropriate for validating novel algorithms
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Things that commonly go wrong

• Poor data quality
• Damaged specimen
• Mis-shapen objects
• Fragments
• Poor image quality
• Noise
• Spectral bleed-through
• Partially-imaged nuclei
• Types of segmentation errors
• Miss
• Inaccurate boundary
• False segmentation
• Under segmentation
• Over segmentation
• Separation errors

Go back to the microscope if at all possible
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Handling Partial Objects

• Usually, they need to be deleted based on their
  features
• Location (close to border)
• Size (less than modeled value)
• Brick Rule
• Define an interior sub-volume in the image
• Only accept cells that are wholly contained in it

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Outlier Detection
Outliers are good candidates for further
inspection
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Color-codes for highlighting errors
Any measure of the quality of fit to the object
model p(X) can serve as a tool for highlighting
errors Red potentially awful Yellow
questionable Green okay
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Explanatory Display Coding

• Make it easy for user to separate unhandled
  errors from handled errors
• One idea is to put mini explanation codes
• Display detailed explanations when a user clicks
  on a cell or rests the mouse
• Keep a record trail of all operations that led
  to each object

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Object Separation Error Example
Gallery view indicates 3 objects
Split Error
Split Cells
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Editing the Output
Add Object

Split/Merge

Dilate/Shrink
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Edit-Based Validation Protocol
Inspect and Edit by observer 1
Supervisory Inspect Edit
Automated Segmentation
Image
Verified Corrected Segmentation
Record of edits
Record of edits
Edits not made are implicitly interpreted as
correct results
Compute Statistics on Recorded Edit Operations
Measure(s) of automated segmentation performance

• Much less effort compared to multi-observer
  validation
• Subtly different from multi-observer validation,
  but a good approximation
• Appropriate for mature algorithms in routine usage

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Algorithm to add an object

• Seeded Region Growing
• User clicks on a point on the object to be added
• Initialize a connected component with this point
• Examine each neighboring pixel
• If the intensity is within X of starting point,
  include that in the connected component
• X tolerance set by user
• Other criteria can be included
• Stop when there are no more points to add
• Flexibility in designing stopping criteria!

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The need to record edits

• Often, cell segmentation is performed in a
  pharmaceutical and/or legal situation
• Much at stake, need protection from cheating and
  carelessness!
• The Food and Drug Administration has laws and
  guidelines, generally called Good Laboratory
  Practices (GLP)
• Bottom Line
• When an edit is made, save the original data, and
  allow rollback (undo)
• Record the time stamp, and identity of the person
  making the edit, and an explanatory note for
  inspector

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Edits are Valuable!

• The edit rate is a direct indicator of software
  performance
• Basis for edit-based validation
• The types of edits indicate the most common types
  of errors being made by the software
• Basis for software revision
• They also indicate the kinds of images and
  objects for which errors are occurring
• Sometimes, a good basis for improving specimen
  preparation and imaging steps

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Summary

• The feature selection problem
• Need to select a few really good ones
• The curse of dimensionality
• Multiple-Observer Validation and performance
  assessment
• Technical dimension
• Human dimension
• Legal dimension

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Instructor Contact Information

• Badri Roysam
• Professor of Electrical, Computer, Systems
  Engineering
• Office JEC 7010
• Rensselaer Polytechnic Institute
• 110, 8th Street, Troy, New York 12180
• Phone [phone]
• Fax [phone]
• Email roysam_at_ecse.rpi.edu
• Website http//www.ecse.rpi.edu/roysam
• Course website http//www.ecse.rpi.edu/roysam/CT
  IA
• Secretary Laraine Michaelides, JEC 7012, (518)
  276 8525, michal_at_.rpi.edu
• Grader Piyushee Jha (jhap_at_rpi.edu)

Center for Sub-Surface Imaging Sensing