frida: an open source framework for image dataset analysis toby cornish, md, phd department of...
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FrIDA:An open source framework for image
dataset analysis
Toby Cornish, MD, PhD
Department of Pathology
Johns Hopkins Medical Institutions
Baltimore, MD
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FrIDAFramework for Image Dataset Analysis
• Framework provides tools that allow users to create their own analysis methods
• Image Dataset iterates over a set of images, applying the same methods to each image
• Analysis returns per image statistics about area and intensity in a given region of interest
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FrIDA specs
• Written in Java
• Uses libraries from the popular Image J program (Wayne Rasband, NIH)
• Programmed by James Morgan
• Design by Toby Cornish, James Morgan and Angelo DeMarzo
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FrIDA specs, cont.
• Licensed under MPL and currently available at sourceforge:– http://sourceforge.net/projects/fridajhu/
• Requirements:– Java 6 runtime environment (JRE)
• Optional:– MySQL database
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FrIDA• Operates on 24 bit color image files, including TIFF,
JPEG, etc.
• Currently supports analysis of:– Area (total, ROI)– Intensity (mean, median, min, max)
• Saves all analysis settings to either an XML file or a MySQL database
• Results are saved to an XML file or plain text file
• Central concept: Masking…
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Masking
• Mask:– a binary image that defines certain pixels
as included (foreground) or excluded (background)
Color Image “Tissue” Mask
Foreground = white
Background = black
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Masking, cont.
• Grayscale segmentation is an example of a process that produces a mask
Color Image “Tissue” Mask
Grayscale segmentation
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Masking, cont.
• FrIDA currently supports these masking methods:
– Color mask: uses HSB color space segmentation to select pixels within a color range
– Lasso mask: freehand selection of pixels using bounding polygons
– Metamask: combination of two masks using boolean logic
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Main FrIDA window
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Masking
• Color mask
• Lasso mask
• Metamask
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Color space segmentation
• Segmentation assigning the pixels in an image to a particular category, i.e. classifying them
• Color segmentation grouping of pixels of similar color– The first step in any analysis of staining, i.e. which
pixels are brown and which are blue?
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HSB/HSV color space• More intuitive for human interaction• 1 pixel = 3 values
– Hue, Saturation, Brightness (Value)– H x S circle (chromaticity)
• Hue defines a color; saturation the amount of color present
– B (V) z-axis• Defines the “brightness”
S
H
0o
S
B
H
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Color space segmentation
S
H = 0 to 35 degrees
S = 0 to 100%
I = 0 to 100% 0
o
35o
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HSB segmentation in FrIDA
• “Color Mask”
• Select colors by either:
– An eyedropper-style tool, and/or
– Three pairs of sliders that define bandpass ranges for Hue, Saturation and Brightness
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Hue: Min > Max Bandstop
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Brown
Color masking, cont.
HSB Segmentation
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Masking
• Color mask
• Lasso mask
• Metamask
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“Lasso” masking
Freehand polygon tool for drawing regions of interest to be masked (red line)
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“Lasso” masking, cont.
Any number of lasso can be defined; multiple selections possible by holding down “shift”
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“Lasso” maskingRed lasso defines a mask
Exclude
Include
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Masking
• Color mask
• Lasso mask
• Metamask
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Meta masking• Metamasks combine two or more masks using
boolean logic:
– AND: the intersection of two masks• “all pixels in both mask1 AND mask2”
– OR: the union of two masks• “all pixels either in mask1 OR mask2”
– NOT: uses the inverse of a mask • “all pixels NOT in mask1”
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Meta masking, cont.• Metamasks combine two or more masks using
boolean logic:
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Meta masking, cont.
• Metamasks bring all the elements together for analysis…
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ExcludeInclude
Include AND (NOT Exclude)
NOT Exclude
NOT
Brown
AND
AND
Include AND (NOT Exclude) AND Brown
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Include AND (NOT Exclude) AND Brown
Original
The mask is applied to the original image, selecting the pixels of interest and resultant image is analyzed
ANALYSIS
MASK
Masked Original
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Future directions
• Preprocessing of images
• Additional masks:– e.g., binary operations
• Erosion, dilation, watershed segmentation, size exclusion, shape descriptor exclusion
• Additional results:– Particle counting
• Integration with TMAJ:– Display of masks while browsing TMAs
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Acknowledgements• James Morgan, B.S.• Bora Gurel, M.D.• Angelo DeMarzo, M.D., Ph.D.
Source for FrIDA can be obtained at sourceforge.net
Anyone interested in a live demo may request one during the meeting