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Tissue Slice Preparation Electrochemical Biosensor Development Microchip Development Fluorescence Video Microscopy Optical Image Chemical Image Composite.

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Presentation on theme: "Tissue Slice Preparation Electrochemical Biosensor Development Microchip Development Fluorescence Video Microscopy Optical Image Chemical Image Composite."— Presentation transcript:

1 Tissue Slice Preparation Electrochemical Biosensor Development Microchip Development Fluorescence Video Microscopy Optical Image Chemical Image Composite Image Analysis Data Acquisition & Processing Microchip Biosensor Array Tissue Sample Biomedical Sciences Chemistry Electrical & Computer Engineering Computer Science Mathematics This program is based upon collaborative work supported by a National Science Foundation Grant No. 0841259; Colorado State University, Thomas Chen, Principal Investigator, Michael A. de Miranda and Stuart Tobet Co-Principal Investigators. Any opinions, findings, conclusions or recommenda- tions expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. C OLORADO H IGH - SCHOOL I NTERDISCIPLINARY P ROJECT Dec. 7, 2010

2 Metamorph (Commercial software) Raw TIF Image Files Analysis Tool (CSU Software) An array of analyzed images, spreadsheets, and data files… ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis

3 Metamorph Raw TIF Image Files

4 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Raw TIF Image File (Time = t) Raw Frame (Time = t, z = 0) Raw Frame (Time = t, z = 1) Raw Frame (Time = t, z = 2) Raw Frame (TIF) (Time = t) MERGE

5 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Equalized (PNG) (Time = t) Raw Frame (TIF) (Time = t) Movie (MOV) Original brightnessAdjusted brightness

6 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Smoothed (PNG) (Time = t) Equalized (PNG) (Time = t) Movie (MOV)

7 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Stabilized (PNG) (Time = t) Smoothed (PNG) (Time = t) Movie (MOV) GOAL: Stabilize the center of the frame…

8 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Cells (PNG) (Time = t) Stabilized (PNG) (Time = t) Movie (MOV) Cell Positions Cell Vectors Tissue Vectors (CSV - Excel)

9 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Trajectories (PNG) (Time = t) Cells (PNG) (Time = t) Movie (MOV) Trajectory Data (CSV - Excel) Raw Data (DAT files)

10 Analysis Tool (CSU Software) ANALYSES: Frame extraction Brightness/contrast Noise filtering Motion compensation Cell identification Trajectory extraction Trajectory analysis Raw Data (DAT files) Report & Summary (CSV - Excel) Diffusion Curve FitsVisual AnalysesRegion detection

11 Acknowledgements: CSU Biomedical Sciences Dept and the Tobet Lab: S. Tobet, M. Stratton, K. Frahm and B. Searcy CSU Department of Mathematics V. Putkaradze University of Ljubljana & Jožef Stefan Institute P. Ziherl The author would like to thank the National Science Foundation for support under Grant No. 0841259.

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