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CyteSeer automatically identifies regions of the image associated with each fiber and calculates are large set of measurements for each fiber. The numbers shown in this image the unique ID's for each fiber. The complete set of measurements are shown in the "Measurement Appendix".

The image and measurements for each fiber can now be manipulated within CyteSeer as needed for a given experiment.

Where the previous figure displayed a set of fiber images for each unique ID, this figure displays a small subset of the measurements available for each fiber.

In this example, we've created a gate to select red fibers of a certain expression level.

A gallery of just the gated red fibers is shown in this figure. This sub-population analysis tool is one of the more powerful CyteSeer features.

This has been a brief demonstration of CyteSeer's automated muscle fiber analysis algorithm.

Short Name    <-------------->    Long Name
Cell ID    <-------------->    ID of each record
Well    <-------------->    Name of the well
Area Mm    <-------------->    Area of Membrane Mask
Area Tm    <-------------->    Area of Thick Membrane Mask
Area Wm    <-------------->    Area of Whole-Cell Mask
Area Fm    <-------------->    Area of Fiber Mask
XLeft Mm    <-------------->    XLeft of Membrane Mask
YTop Mm    <-------------->    YTop of Membrane Mask
Width Mm    <-------------->    Width of Membrane Mask
Height Mm    <-------------->    Height of Membrane Mask
IsBoundary Mm    <-------------->    IsBoundary of Membrane Mask
XCentroid Mm    <-------------->    XCentroid of Membrane Mask
YCentroid Mm    <-------------->    YCentroid of Membrane Mask
XLeft Tm    <-------------->    XLeft of Thick Membrane Mask
YTop Tm    <-------------->    YTop of Thick Membrane Mask
Width Tm    <-------------->    Width of Thick Membrane Mask
Height Tm    <-------------->    Height of Thick Membrane Mask
IsBoundary Tm    <-------------->    IsBoundary of Thick Membrane Mask
XCentroid Tm    <-------------->    XCentroid of Thick Membrane Mask
YCentroid Tm    <-------------->    YCentroid of Thick Membrane Mask
XLeft Wm    <-------------->    XLeft of Whole-Cell Mask
YTop Wm    <-------------->    YTop of Whole-Cell Mask
Width Wm    <-------------->    Width of Whole-Cell Mask
Height Wm    <-------------->    Height of Whole-Cell Mask
IsBoundary Wm    <-------------->    IsBoundary of Whole-Cell Mask
XCentroid Wm    <-------------->    XCentroid of Whole-Cell Mask
YCentroid Wm    <-------------->    YCentroid of Whole-Cell Mask
XLeft Fm    <-------------->    XLeft of Fiber Mask
YTop Fm    <-------------->    YTop of Fiber Mask
Width Fm    <-------------->    Width of Fiber Mask
Height Fm    <-------------->    Height of Fiber Mask
IsBoundary Fm    <-------------->    IsBoundary of Fiber Mask
XCentroid Fm    <-------------->    XCentroid of Fiber Mask
YCentroid Fm    <-------------->    YCentroid of Fiber Mask
Cell Mean Radius    <-------------->    Cell Mean Radius
Cell Perimeter    <-------------->    Cell Perimeter
Cell Roundness    <-------------->    Cell Roundness
Boundary Cell    <-------------->    Boundary Cell
X-Cell    <-------------->    X-Position of Cell
Y-Cell    <-------------->    Y-Position of Cell
Cell Major Axis    <-------------->    Major Axis of Cell
Cell Minor Axis    <-------------->    Minor Axis of Cell
Cell Elongation    <-------------->    Elongation of Cell
Fiber Mean Radius    <-------------->    Fiber Mean Radius
Fiber Perimeter    <-------------->    Fiber Perimeter
Fiber Roundness    <-------------->    Fiber Roundness
X-Fiber    <-------------->    X-Position of Fiber
Y-Fiber    <-------------->    Y-Position of Fiber
Fiber Major Axis    <-------------->    Major Axis of Fiber
Fiber Minor Axis    <-------------->    Minor Axis of Fiber
Fiber Elongation    <-------------->    Elongation of Fiber
TII Mi Mm    <-------------->    Total Integrated Intensity of Muscle Image on Membrane Mask
API Mi Mm    <-------------->    Average Pixel Intensity of Muscle Image on Membrane Mask
MPI Mi Mm    <-------------->    Median Pixel Intensity of Muscle Image on Membrane Mask
SPI Mi Mm    <-------------->    Standard Deviation of Pixel Intensity of Muscle Image on Membrane Mask
TII Mi Tm    <-------------->    Total Integrated Intensity of Muscle Image on Thick Membrane Mask
API Mi Tm    <-------------->    Average Pixel Intensity of Muscle Image on Thick Membrane Mask
MPI Mi Tm    <-------------->    Median Pixel Intensity of Muscle Image on Thick Membrane Mask
SPI Mi Tm    <-------------->    Standard Deviation of Pixel Intensity of Muscle Image on Thick Membrane Mask
Cell Muscle Integrated Intensity    <-------------->    Total Integrated Muscle Intensity on Cell
Cell Muscle Average Intensity    <-------------->    Average Muscle Intensity on Cell
Cell Muscle Std Dev Intensity    <-------------->    Standard Deviation of Muscle Intensity on Cell
Cell Skew Intensity    <-------------->    Skewness of Muscle Intensity on Cell
Cell Kurtosis Intensity    <-------------->    Kurtosis of Muscle Intensity on Cell
Cell TII to StdDev Ratio    <-------------->    Ratio of Muscle Integrated Intensity to Muscle Standard Deviation on Cell
Fiber Muscle Integrated Intensity    <-------------->    Total Integrated Muscle Intensity on Fiber
Fiber Muscle Average Intensity    <-------------->    Average Muscle Intensity on Fiber
Fiber Muscle Std Dev Intensity    <-------------->    Standard Deviation of Muscle Intensity on Fiber
Fiber Skew Intensity    <-------------->    Skewness of Muscle Intensity on Fiber
Fiber Kurtosis Intensity    <-------------->    Kurtosis of Muscle Intensity on Fiber
Fiber TII to StdDev Ratio    <-------------->    Ratio of Muscle Integrated Intensity to Muscle Standard Deviation on Fiber
Protein-1 TII    <-------------->    Total Integrated Intensity of Protein-1
Protein-1 API    <-------------->    Average Intensity of Protein-1
Protein-1 MPI    <-------------->    Median Intensity of Protein-1
Protein-1 SPI    <-------------->    SD Intensity of Protein-1
Protein-1 Skewness    <-------------->    Skewness of Intensity of Protein-1
Protein-1 Kurtosis    <-------------->    Kurtosis of Intensity of Protein-1
Protein-1 Edge TII    <-------------->    Total Integrated Edge Intensity of Protein-1
Protein-1 Edge API    <-------------->    Average Edge Intensity of Protein-1
Protein-1 Edge MPI    <-------------->    Median Edge Intensity of Protein-1
Protein-1 Edge SPI    <-------------->    SD Edge Intensity of Protein-1

Vala Sciences is a cell biology company offering software, kits, services and custom development for analyzing a wide variety of cell types and conditions from adipocytes & stem cells to primary & well established cell lines.
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CyteSeer is a registered trademark of Vala Sciences Inc. All rights reserved 2005-2009.

Many thanks to Chris Mendias and Konstantin Bakurin at the University of Michigan for the representative images.