PG-4035, Virtual Microscopy in the cloud, by Wojciech Tarnawski

1 | PRESENTATION TITLE | NOVEMBER 21, 2013 | CONFIDENTIAL

VIRTUAL MICROSCOPY IN THE CLOUD WOJCIECH TARNAWSKI , CSO

MICROSCOPEIT LTD.


Virtual Microscopy in the Cloud Wojciech Tarnawski, PhD, CSO MicroscopeIT Ltd., Wroclaw, Poland


MICROSCOPY IS COMPLICATED

!  Different formats, different producers.

!  Different software for different image processing tasks.

!  Image analysis takes time.

!  Open Source vs. Commercial Software.

!  Image types: 2D (fluorescence, phase-contrast), 3D (confocal), 4D (3D objects in time), different channels targeting different molecular elements.

CreaMve Commons 2.0, Nicole Yeary's photos via GeRy Images


WHAT IS VIRTUM?

Cloud Computing Image processing pipeline integrated accessed in the web browser.

Flexibility All formats, dimensions and modality supported

Acceleration Time consuming image analysis ported to GPU.

Information Retrieval Phenotype detection of biologically relevant information directly from images.

Robust and fast workflow-based image analysis Save time thanks to intelligent algorithms with „visual” development.

Image credit: leverhawk.com, Why is cloud integraMon sMll an adopMon barrier, 2012.


IN ACTION

Our system: 32 GPU cards (6 donated by AMD)

Database

Data acquisi:on

" Work-‐flow based image processing and task scheduling


FEATURES, APPLICATIONS Visualization (Virtual Microscopy)

Data Analysis

E-learning

Teleconferencing teleconsultations

High-Content and High-Throughput

Screening

Quantitative data analysis

Scientific research

Clinical trials

Biotechnology

Medicine and biology


Visualiza:on 2D Image Series WSI VisualizaMon 3D Image Series Movie ProjecMon 3D Geometry Viewer Rendering ReconstrucMon

Input Data Types

Not Ordered WSI Image z-‐stacks Time-‐Lapse Time-‐Lapse Images ( Image Pyramids) Image Series Z-‐Stacks


INPUT DATA TYPES : NOT-‐ORDERED SETS AND TIME-‐LAPSE IMAGE SERIES


INPUT DATA TYPES : Z-‐STACKS AND TIME-‐LAPSE Z-‐STACKS


INPUT DATA TYPES : IMAGE PYRAMID


Visualiza:on 2D Image Series WSI VisualizaMon 3D Image Series Movie ProjecMon 3D Geometry Viewer Rendering ReconstrucMon

Data Analysis 2D Image Processing 2-‐3D Image ReconstrucDon Time-‐Dependent Analysis Post-‐Processing and Analysis

Image Processing and Analysis Library

2-‐3D Mesurements Image Preprocessing 2-‐3D Object SegmentaDon 2-‐3D Object Analysis StaDsDcs

Input Data Types

Not Ordered WSI Image z-‐stacks Time-‐Lapse Time-‐Lapse Images ( Image Pyramids) Image Series Z-‐Stacks


CLOUD COMPONENTS (BACK-‐END) 1/3 Image Processing and Analysis Library : about 70 methods tailored for microscopy imaga data implemented on CPU and GPU

2-‐3D Mesurements

Image Preprocessing : noise removal, contrast improvement, inhomogeneous lighDng removal, opDcal deconvoluDon, 2-‐3D Image SDtching, Histogram-‐based processing, MulD-‐channel Image Composing, Image ArithmeDc, Edge DetecDon, … etc.

2-‐3D Object SegmentaDon : automaDc or machine-‐learning methods for segmentaDon of 2-‐3D objects e.g. 2-‐3D Cell Tracking Advanced SegmentaDon in mulD-‐dimensional space composed with texture and color features, AcDve Contour and AcDve Mesh, Threshold -‐ and Morphology – based SegmentaDon, Mean-‐Shi[, …

2-‐3D Object Analysis : Split into 2-‐3D Ellipsoids e.g. for highly clustered cells , Morphology Operatos , Weighted Distance Transform, Voronoi TriangulaDon, Object RecogniDon module for Cell Phase ClassificaDon by Markov chains

StaDsDcs Module – PCA, Basic StaDsDcs, Cluster Analysis,


3D IMAGE SEGMENTATION : ACTIVE MESH


CLOUD COMPONENTS (BACK-‐END) 1/3 Image Processing and Analysis Library : about 70 methods tailored for microscopy imaga data implemented on CPU and GPU

* A Robust Algorithm for Segmen:ng and Tracking Clustered Cells in Time-‐Lapse Fluorescent Microscopy Tarnawski, W. ; Kurtcuoglu, V. ; Lorek, P. ; Bodych, M. ;RoRer, J. ; Muszkieta, M. ; Piwowar, L. ; Poulikakos, D. ;Majkowski, M. ; Ferrari, A. Biomedical and Health InformaMcs, IEEE Journal of Volume: 17 , Issue: 4 PublicaMon Year: 2013 , Page(s): 862 -‐ 869

Workflow-‐based image processing


WORKFLOW – BASED IMAGE PROCESSING AND ANALYSIS


USE CASES

!  Detection of nuclei and cytoplasm in 80 000 images (512x512 pixels) takes about 2 hours on multi-core CPU (AMD Athlon(tm) II X4 640 Processor). GPU provided up to 4x acceleration

!  Optical deconvolution : about 25x acceleration for 512x512 image

!  3D-dimensional diffuse filter on image-stack (z-stack with 1920x1080) : about 10x acceleration


CLOUD COMPONENTS (BACK-‐END) 2/3

Image Processing and Analysis Library : about 70 methods tailored for microscopy imaga data implemented on CPU and GPU

Task Scheduler to provide image analysis results for many users.

Scheduling approach :

Scheduler –> Executor –> Worker –> Task

-‐ Schedules image processing tasks on the CPU & GPU cluster. -‐ Monitors CPU, GPU, memory, storage usage. -‐ OpMmizes scalability.


Image Processing and Analysis Library : about 70 methods tailored for microscopy imaga data implemented on CPU and GPU

Task Scheduler to provide image analysis results for many users.

Database Module -‐ to store the microscopic image data

Database Module provides upload data module that supports:

•  about 100 microscopic image data formats (i.e. lsm, nd2, oly, mulD-‐channel , 16-‐bit Dff, basic graphic formats, …)

•  compressed images series (zip)

•  filename parser to upload image series ordered by channel, z-‐stack layers, Dme-‐points, …

•  users data are fully organized

•  users can be assigned to many projects

CLOUD COMPONENTS (BACK-‐END) 3/3


PROJECT DATA ORGANIZATION


CLIENT (GUI) COMPONENTS

Graphical User Interface (GUI) installed as a plugin in the web browser:

!  Designed for touch-‐based devices.

!  Designed to tag microscopic image series with metadata.

!  Includes different viewers to visualize mulM-‐dimensional images.

!  Provides „visual” interface to design the workflow for image processing and analysis.

!  Provides tools to select the image regions for futher iamge analysis.


!  MicroscopeIT Ltd. Kutnowska 1-‐2 Wroclaw, Poland

!  Contact: [email protected] Tel. +48 605 111 445

Skype:tar_woj


DISCLAIMER & ATTRIBUTION

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ATTRIBUTION

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PG-4035, Virtual Microscopy in the cloud, by Wojciech Tarnawski

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