frida: an open source framework for image dataset analysis toby cornish, md, phd department of...

FrIDA:An open source framework for image

dataset analysis

Toby Cornish, MD, PhD

Department of Pathology

Johns Hopkins Medical Institutions

Baltimore, MD

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

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

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

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…

Masking

• Mask:– a binary image that defines certain pixels

as included (foreground) or excluded (background)

Color Image “Tissue” Mask

Foreground = white

Background = black

Masking, cont.

• Grayscale segmentation is an example of a process that produces a mask

Color Image “Tissue” Mask

Grayscale segmentation

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

Main FrIDA window

Masking

• Color mask

• Lasso mask

• Metamask

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?

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

Color space segmentation

S

H = 0 to 35 degrees

S = 0 to 100%

I = 0 to 100% 0

o

35o

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

Hue: Min > Max Bandstop

Brown

Color masking, cont.

HSB Segmentation

Masking

• Color mask

• Lasso mask

• Metamask

“Lasso” masking

Freehand polygon tool for drawing regions of interest to be masked (red line)

“Lasso” masking, cont.

Any number of lasso can be defined; multiple selections possible by holding down “shift”

“Lasso” maskingRed lasso defines a mask

Exclude

Include

Masking

• Color mask

• Lasso mask

• Metamask

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”

Meta masking, cont.• Metamasks combine two or more masks using

boolean logic:

Meta masking, cont.

• Metamasks bring all the elements together for analysis…

ExcludeInclude

Include AND (NOT Exclude)

NOT Exclude

NOT

Brown

AND

AND

Include AND (NOT Exclude) AND Brown

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

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

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