Download - Tissue Slice Preparation
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Tissue Slice Preparation
ElectrochemicalBiosensor
Development
MicrochipDevelopment
FluorescenceVideo Microscopy
Optical Image
Chemical Image
Composite Image
Analysis
Analysis
Data Acquisition &
Processing
Microchip
Biosensor Array
Tissue Sample
Biomedical SciencesChemistryElectrical & Computer EngineeringComputer ScienceMathematics
This program is based upon collaborativework 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.
COLORADO HIGH-SCHOOLINTERDISCIPLINARY
PROJECT
Dec. 7, 2010
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Automated Analysis of Image SetsMetamorph
(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
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Automated Analysis of Image SetsMetamorph
Raw TIF Image Files
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Automated Analysis of Image SetsAnalysis 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
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Automated Analysis of Image SetsAnalysis 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 brightness Adjusted brightness
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Automated Analysis of Image SetsAnalysis 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)
}
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Automated Analysis of Image SetsAnalysis 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…
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Automated Analysis of Image SetsAnalysis 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 PositionsCell Vectors
Tissue Vectors(CSV - Excel)
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Automated Analysis of Image SetsAnalysis 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)
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Automated Analysis of Image SetsAnalysis 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 Fits Visual AnalysesRegion detection
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Automated Analysis of Image SetsAcknowledgements:
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.