image analysis of kidney biopsies using image –mining framework

Visvesvaraya Technological UniversityJnanasangama, Belgaum

Rajiv Gandhi Institute of Technology

Cholanagar, RGC Campus, RT Nagar,

Bangalore, Karnataka 560 032

Technical Seminar 2014Department of

biomedical engineering

Image analysis of kidney biopsies using image –mining framework

D Vinayakam(1rg10bm008)

Content:

Introduction

Image Mining

Need For Implementation

Objective

Block Diagram

INTRODUCTION

Definition Function Location

Causes Symptoms

Definition

Definition

Kidney BiopsyTypes Indications

Contradictions Procedure Complication

Types:

1. Native Renal Biopsy

2. Transplant Renal Biopsy

Indications

1. Haematuria

2. Proteinuria

3. Renal Failure

Contradictions

1. Absolute

2. Relative

Procedure

1. Before Biopsy

2. During Biopsy

3. After Biopsy

Complications

Image Mining

Definition

Process

1. Image Features

2. Function

3. Other Shapes

Colour Shapes Textures

Functions Gabor Functions

Other Shapes

Morphological

Closing

Morphological

Opening

Block Diagram

User Action

Define Image

Processing Task

Select

Workflow

Manageme

nt tool

Select

Operat

ors

Taverna

Rapid minner

Framework automation

Taverna

Image file

Work Flow Inputs

Transform Image

Input (1,n)

Transform Image

Output (1,n)

Encode Byte

Array To Base 64Upload Image

InputUpload Image Output

Convert To

8 Bit

Angiogenesis

Extraction

Adaptive

Threshold

Convert To

Binary

Extract

Features Input

Extract Features

Output

Skeletonize

Image

Image Features Skeletonised Image Initial Image

Get Image URL Input

Get Image URL Output

Get Image URL

2 Input

Get Image URL

2 Output

Work Flow Outputs

2 31

4

56

7

8

9

Rapid minner

Case Study Application

Kidney Biopsy

Image Training Set

Kidney Biopsy

Image Test Set

Segmentation

Squares Feature

Extraction

Ground Truth

Training

Segmentation Segmentation

Squares Feature

Characterization

Morphological

Operator

(Majority Voting)

Non Pathogenic

Glomerulus

Pathogenic

Tubulus

Non Pathogenic

Tubulus

Pathogenic

Glomerulus

Object

Detection

Trained Model