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Virtum: virtual microscopy in the cloud

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MicroscopeIT

on 26 August 2016

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Transcript of Virtum: virtual microscopy in the cloud

Microscopy is complicated
Different formats, different producers

Different software for different image processing tasks

Image analysis takes time

Open Source vs Commercial Software
What is Virtum?
Cloud Computing

Image processing pipeline accessed in the web browser.
Robust and fast workflow-based image analysis

Intelligent algorithms that „learn” on the fly.

Acceleration

Time consuming image analysis ported to GPU.

Flexibility

All formats, dimensions and modality supported
Information Retrieval

Example: phenotype detection of biologically relevant information directly from images.

Virtum in action
What's the deal?
About Virtum
Data aquisition
Image processing
Our system
According to our knowledge, there is no SaaS-type solution, based on e-services offered in our target segments. Therefore, MicroscopeIT services will compete with standalone image processing software.

Currently, there is no leader for the whole market of microscope image analysis software. There are many companies offering systems for the analysis of microscope images desktop software, often dedicated to specific data formats of the manufacturer.

Microscopy is complicated

BENEFITS:
Single-point access to microscopic data in a standardized way, increased performance by the use of GPUs, cost reduction by using SaaS model.
CellScope
Work-flow based image processing and task scheduling

32 GPU
CARDS
Virtum Features
Visualization (Virtual Microscopy)

Data Analysis
Medicine and biology

Clinical trials

Scientific research
Biotechnology
E-learning
Teleconferencing
teleconsultations

Quantitative data
analysis

High-Content and
High-Throughput
Screening
Visualisation
Input Data Types

Image Processing Library

2-3D Mesurements
Image Preprocessing
2-3D Object Segmentation
2-3D Object Analysis
Statistics
2D Image Processing
2-3D Image Reconstruction
Time-Dependent Analysis
Post-Processing and Analysis
z-stacks sample
CLOUD Components (BACK-END) 1/4

Image Processing and Analysis Library:
about 70 methods tailored for microscopy image data implemented on CPU and GPU in 2D and 3D.

Image Preprocessing:
noise removal, contrast improvement, inhomogeneous lighting removal, optical deconvolution, 2-3D Image Stitching, Histogram-based processing, Multi-channel Image Composing, Image Arithmetic, Edge Detection, … etc.

2-3D Object Segmentation:
automatic or machine-learning methods for segmentation of 2-3D objects e.g. 2-3D Cell Tracking Advanced Segmentation in multi-dimensional space composed with texture and color features, Active Contour and Active Mesh, Threshold - and Morphology – based Segmentation, Mean-Shift, … etc.

2-3D Object Analysis:
Split into 2-3D Ellipsoids e.g. for highly clustered cells , Morphology Operatos , Weighted Distance Transform, Voronoi Triangulation, Object Recognition module for Cell Phase Classification by Markov chains, ... etc.

Statistics Module:
PCA, Basic Statistics, Cluster Analysis, ... etc.


CLOUD Components (BACK-END) 2/4
Workflow-based image processing
IN
SEG
Weighted
Distance Transform
Img2RLC
Split Ellipses
2D
Ellipses ROI
Image Processing and Analysis Library : about 80 methods tailored to microscopy imaga data implemented on CPU and GPU

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


CLOUD Components (BACK-END) 3/4

Image Processing and Analysis Library : about 80 methods tailored for microscopy imaga data implemented on CPU and GPU

Task Scheduler to provide image analysis to many users.

Scheduling approach :





Schedules image processing tasks on the CPU & GPU cluster.

Monitors CPU, GPU, memory, storage usage.

Optimizes scalability.
CLOUD Components (BACK-END) 4/4

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

Task Scheduler to provide image analysis to 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, multi-channel , 16-bit tiff, basic graphic formats, …),

Compressed images series (zip),

Filename parser to upload image series ordered by channel, z-stack layers, time-points,

Users data are fully structured.

Users can be assigned to many projects


Client (GUI) components
Graphical User Interface (GUI)

Supporting touch-based devices

Designed to tag microscopic image series with metadata

Includes different viewers to visualize multi-dimensional images

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

Provides tools to select the image regions for futher image analysis



MicroscopeIT Ltd.
Kutnowska 1-2, Wroclaw, Poland


Contact:

info@microscopeit.com
http://www.microscopeit.com



1/2
2/2
1
2
1/3
2/3
3/3
Database
2D Image Series
3D Geometry
Reconstruction
WSI Visualization
Viewer
3D Image Series
3D Image Series
Rendering
Input Data Types
Not Ordered
WSI
Image z-stacks
Time-Lapse
Time-Lapse
Images
(Image Pyramids)
Image Series
Z-Stacks
Visualisation
4
Data analysis in the cloud
5
Data management
3
Scheduler –> Executor –> Worker –> Task
Virtual Microscopy in the Cloud
Full transcript