Dynamic time warping for automated cell cycle labelling
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Dynamic Time Warping for Automated Cell Cycle Labelling. A. El-Labban, A. Zisserman University of Oxford. Y. Toyoda, A. Bird, A. Hyman Max Planck Institute of Molecular Cell Biology and Genetics. Objectives. Segment and track mitotic cells Label mitotic phases Fully automated system.

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Dynamic Time Warping for Automated Cell Cycle Labelling

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Dynamic time warping for automated cell cycle labelling

Dynamic Time Warping for Automated Cell Cycle Labelling

A. El-Labban, A. Zisserman

University of Oxford

Y. Toyoda, A. Bird, A. Hyman

Max Planck Institute of Molecular Cell Biology and Genetics


Objectives

Objectives

  • Segment and track mitotic cells

  • Label mitotic phases

  • Fully automated system

Interphase

Prometaphase

Anaphase

Telophase

Prophase

Metaphase


Dynamic time warping for automated cell cycle labelling

Data

  • 3D time lapse image stacks

  • Use max intensity z-projections

  • 1-5 minute temporal resolution

  • 0.2 micron xy-resolution


Approach

Approach

  • Existing approaches (e.g. Harder et al. 2009, Held et al. 2010 [CellCognition]):

    • Track cells

    • Label cell cycle phase frame-by-frame

    • Smooth result with HMM (CellCognition)

  • Our Approach:

    • Track cells

    • Label all frames by using temporal signals of features


Temporal signals of features

Temporal signals of features


Temporal signals of features1

Temporal signals of features

Anaphase

Interphase

Prometaphase

Telophase

Prophase

Metaphase


Overview

Overview

  • Part I

    • Track cells in videos

  • Part II

    • Label mitotic phases


Part i tracking

Part I – Tracking


Tracking

Tracking

  • Tracking by detection

    • Detect first, then associate objects

    • Here we use detection by classification.


Segmentation our approach

Segmentation: Our approach

  • Logistic regression classifier

  • Graph Cuts

Logistic regression

classifier

Graph Cut

Input image

Probability map

Binary map


Logistic regression classifier

Logistic Regression Classifier

  • Feature:

    • 10 bin intensity histogram in 5x5 window around pixel

    • Non-uniform bins

    • Get local neighbourhood information as opposed to single pixel

    • Histogram gives rotational invariance


Logistic regression

Logistic Regression

  • Gives a probability map:


Graph cuts

Graph Cuts

Gradient dependent pairwise term

Probability from Logistic Regression Classifier

  • Uses local neighbourhood information to make decisions

  • Pairwise term penalises different labels for adjacent pixels


Graph cuts1

Graph Cuts


Tracking1

Tracking

  • Associate objects based on distance between centroids in consecutive frames.

  • Easy given segmentation and slow movement of cells.


Tracking2

Tracking

  • Associate objects based on distance between centroids in consecutive frames.

  • Easy given segmentation and slow movement of cells.


Tracking3

Tracking

  • Associate objects based on distance between centroids in consecutive frames.

  • Easy given segmentation and slow movement of cells.


Tracking4

Tracking


Part ii phase labelling

Part II – Phase Labelling


Simple features

Simple features

  • Maximum Intensity:

Interphase


Simple features1

Simple features

  • Maximum Intensity:

Interphase

Prophase


Simple features2

Simple features

  • Maximum Intensity:

Interphase

Prometaphase

Prophase


Simple features3

Simple features

  • Maximum Intensity:

Interphase

Prometaphase

Prophase

Metaphase


Simple features4

Simple features

  • Maximum Intensity:

Anaphase

Interphase

Prometaphase

Prophase

Metaphase


Simple features5

Simple features

  • Maximum Intensity:

Anaphase

Interphase

Prometaphase

Prophase

Metaphase


Simple features6

Simple features

  • Maximum Intensity:

Anaphase

Interphase

Prometaphase

Telophase

Prophase

Metaphase


Reference signal

Reference signal

  • Average over training set (±1 standard deviation shaded):


Dynamic time warping

Dynamic time warping

  • Stretch signal onto labelled reference:


Dynamic time warping1

Dynamic time warping

  • Stretch signal onto labelled reference:


Dynamic time warping2

Dynamic time warping

Anaphase

Interphase

Prometaphase

Interphase

Telophase

Prophase

Metaphase


Dynamic time warping3

Dynamic time warping

  • Find a cost matrix of pairwise distances between points on the two signals

  • Find minimum cost path through matrix

Test Signal

Reference Signal


Features

Features

  • Use 3 features and their gradients at two different scales:

    • Maximum intensity

    • Area

    • Compactness ( )


Hidden markov model

Hidden Markov Model

  • Hidden states, x

    • Mitotic phases

  • Observations, y

    • Features

  • Transition probabilities, a

    • From one phase to the next

  • Emission probabilities, b

    • Of features having a given value in a given phase

Image: http://en.wikipedia.org/wiki/Hidden_Markov_model


Hidden markov model1

Hidden Markov Model

  • DTW essentially a special case of HMM

  • Easy to extend approach

  • Can add other classes e.g. cell death

  • Split phases into sub-phases to account for variation


Experiments and data

Experiments and Data

  • 54 movies

  • 119 mitotic tracks

  • 27 movies (61 tracks) training, 27 movies (58 tracks) testing


Results

Results

Interphase

Prophase

Prometaphase

Metaphase

Anaphase

Telophase


Results1

Results


Outputs

Outputs


Outputs1

Outputs

  • Synopsis video1 of mitotic cells

  • Aligned to start of anaphase

1Rav-Acha et al., 2006


Conclusions

Conclusions

  • Novel approach to cell cycle phase labelling

  • Utilises temporal context

  • Extendable with HMM


Questions

Questions?


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