Why is this(*) Standard Different From All Other Standards(**)

1
Why is this() Standard Different From All Other
Standards()
Standards have become so popular that every
society wants to make one for themselves
Anonymous
Ilya Ravkin Imaging Consultant www.ravkin.net
() The proposed SBS Image and Data Exchange
Standard for HCS/HCA () Related Standards
dealing with Images and Data see below
2
Related Standards
The nice thing about standards is that there are
so many of them from which to choose - Andrew
Tannenbaum (http//www.sysprog.net/quotes.html)
OME - Open Microscopy Environment
(http//www.openmicroscopy.org/index.html) 
MIACA - Minimum Information About a Cellular
Assay (http//miaca.sourceforge.net/)  Libics -
Image Cytometry Standard (http//libics.sourceforg
e.net) CytometryML (http//www.newportinstrument
s.com/cytometryml/cytometryml.htm) MIAME -
Minimum information about a microarray experiment
(http//www.mged.org/Workgroups/MIAME/miame.html)
MISFISHIE - Minimum Information Specification
For In Situ Hybridization and Immunohistochemistry
Experiments (http//mged.sourceforge.net/misfishi
e/) The Tissue Microarray Data Exchange
Specification (http//www.biomedcentral.com/1472-6
947/3/5) Bioinformatics Standards for Flow
Cytometry (http//flowcyt.sourceforge.net/) FCS
- Flow Cytometry Standard (http//www.isac-net.org
) Association for Pathology Informatics
Standards (http//www.pathologyinformatics.org/sta
ndards.htm) DICOM - Digital Imaging and
COmmunications in Medicine (http//medical.nema.or
g/dicom/2003.html) LDIP - Laboratory Digital
Imaging Project (http//www.ldip.org/)
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What is the Purpose of These Standards? - 1
Following are the stated goals of these standards
quoted from respective web sites or published
articles.
The Open Microscopy Environment (OME) Data Model
and XML file open tools for informatics and
quantitative analysis in biological imaging
Genome Biology, 2005, 6R47 Ilya G Goldberg,
Chris Allan, Jean-Marie Burel, Doug Creager,
Andrea Falconi, Harry Hochheiser, Josiah
Johnston, Jeff Mellen, Peter K Sorger and Jason R
Swedlow To make it possible to manipulate and
share image data as readily as genomic data, we
are building an image-management system geared to
the specific needs of quantitative microscopy.
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What is the Purpose of These Standards? - 2
http//www.mged.org/Workgroups/MIAME/miame.html
MIAME describes the Minimum Information About a
Microarray Experiment that is needed to enable
the interpretation of the results of the
experiment unambiguously and potentially to
reproduce the experiment.
http//miaca.sourceforge.net We propose the
Minimum Information About a Cellular Assay
(MIACA), and develop this as an information
guideline and a modular Cellular Assay Object
Model (CA-OM) that is capable of covering the
range of cellular assays possible and which is
the basis for efficient data exchange.
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What is the Purpose of These Standards? - 3
MISFISHIE - Minimum Information Specification For
In Situ Hybridization and Immunohistochemistry
Experiments (http//mged.sourceforge.net/misfishie
) This specification details the minimum
information that should be provided when
publishing, making public, or exchanging results
from visual interpretation-based tissue gene
expression localization experiments such as in
situ hybridization, immunohistochemistry,
reporter construct genetic experiments (GFP/green
fluorescent protein, beta-galactosidase), etc..
Compliance to this standard is expected to
provide researchers at other labs enough
information to reproduce the experiment and/or to
fully evaluate the data upon which results are
based.
http//www.ldip.org The Laboratory Digital
Imaging Project (LDIP) was developed under the
direction of the Association for Pathology
Informatics (API) to develop and promote the use
of pathology images to improve patient care and
improve the quality of research in pathology by
the development of standards relating to the
interchange of various types of images.
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What is the Purpose of These Standards? - 4
The tissue microarray data exchange
specification A community-based, open source
tool for sharing tissue microarray data BMC
Medical Informatics and Decision Making 2003,
35 Jules J Berman, Mary E Edgerton and Bruce A
Friedman Without such a specification, TMA data
files can not be shared or merged, and the full
scientific value of this new technology is not
realized.
http//www.newportinstruments.com/cytometryml/cyto
metryml.htm Cytology automation and research
will be enhanced by the creation of a common data
format. This data format would provide the
pathology and research communities with a uniform
way for annotating and exchanging images, flow
cytometry, and associated data.
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Purpose of the SBS Image And Data Exchange
Standard for HCS/HCA
All of the related standards attempt to
adequately describe the collected data and
facilitate data sharing and pooling among
different organizations, hence the names minimal
information about .  In the academic world and
for the advancement of science the comprehensive
description of data is necessary and should be
enforced either by the standard itself or by some
acceptance body, e.g. magazine editors.  Our
goal at SBS should be not data sharing among
different organizations, but interoperability of
software from different vendors, which will give
greater flexibility to the user. The question of
how well or badly the experiment is described and
which terms are used for this description should
be left entirely in the authority of the user (or
the users company).   This change in purpose
has a lot of technical consequences.  We do not
need to agree on numerous fields, tags,
vocabularies, and ontologies. All that is needed,
is to agree on the syntax and computer
representation.  It is almost universally
accepted today that XML is the best way to
describe this kind of data.  The task now becomes
quite manageable to agree on how to parse or
update the XML file in order to get access to
images, associated with them descriptors, and
derived from them numerical results.
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The Difference
Other Standards
This Standard
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Example of Information Flow in HCS/HCA Image
Acquisition and Image and Data Analysis
Company B Data Entry Application
(If there was a standard)
Company A Imager
Before Image Acquisition SampleLayout.xml
SamplePlate.xml After Image Acquisition
Company C Image Analysis SW
SamplePlate.xml After First Image Analysis
Company D Data Analysis SW
Company E Image Analysis SW
SamplePlate.xml After Second Image Analysis
Company F Data Analysis SW
Satisfied
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SampleLayout.xml
ltPlateLayoutgt ltPlateLayoutIDgtSAMPLE_LAYOUTlt/Plate
LayoutIDgt ltWellgt   ltWellNumgt1lt/WellNumgt  
ltDrugIDgtLY294002lt/DrugIDgt   ltDosegt0.001lt/Dose
gt   ltCellTypegtMCF7lt/CellTypegt  
lt/Wellgt lt!-- other wells here   --gt
lt/PlateLayoutgt
One Well
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SamplePlate.xmlAfter Image Acquisition
ltPlategt ltPlateIDgtSAMPLE_PLATElt/PlateIDgt
ltPlateLayoutIDgtSAMPLE_LAYOUTlt/PlateLayoutIDgt
ltWellgt ltWellNumgt1lt/WellNumgt
ltChannelgt ltChannelIDgtGFPlt/ChannelIDgt
ltChannelImagegtC\SAMPLE_PLATE\W01-Green.TIFlt/C
hannelImagegt lt/Channelgt ltChannelgt ltChannel
IDgtDRAQ5lt/ChannelIDgt ltChannelImagegtC\SAMPLE_P
LATE\W01-Red.TIFlt/ChannelImagegt
lt/Channelgt lt/Wellgt lt!-- other wells here  
--gt lt/Plategt
One Well
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SamplePlate.xmlAfter First Image Analysis
ltPlategt ltPlateIDgtSAMPLE_PLATElt/PlateIDgt
ltPlateLayoutIDgtSAMPLE_LAYOUTlt/PlateLayoutIDgt
ltWellgt ltWellNumgt1lt/WellNumgt
ltChannelgt ltChannelIDgtGFPlt/ChannelIDgt
ltChannelImagegtC\SAMPLE_PLATE\W01-Green.TIFlt/C
hannelImagegt lt/Channelgt ltChannelgt ltChannel
IDgtDRAQ5lt/ChannelIDgt ltChannelImagegtC\SAMPLE_P
LATE\W01-Red.TIFlt/ChannelImagegt
lt/Channelgt ltMeasuregt   ltMeasureNamegtMEASUR
E_1lt/MeasureNamegt   ltMeasureMethodgtFIRST_METHO
Dlt/MeasureMethodgt   ltMeasureMethodParametersgt1
20 0.5 30lt/MeasureMethodParametersgt  
ltMeasureValuegt0.73lt/MeasureValuegt  
lt/Measuregt lt/Wellgt lt!-- other wells here  
--gt lt/Plategt
Added
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SamplePlate.xmlAfter Second Image Analysis
ltPlategt ltPlateIDgtSAMPLE_PLATElt/PlateIDgt
ltPlateLayoutIDgtSAMPLE_LAYOUTlt/PlateLayoutIDgt
ltWellgt ltWellNumgt1lt/WellNumgt
ltChannelgt ltChannelIDgtGFPlt/ChannelIDgt
ltChannelImagegtC\SAMPLE_PLATE\W01-Green.TIFlt/C
hannelImagegt lt/Channelgt ltChannelgt ltChannel
IDgtDRAQ5lt/ChannelIDgt ltChannelImagegtC\SAMPLE_P
LATE\W01-Red.TIFlt/ChannelImagegt
lt/Channelgt ltMeasuregt   ltMeasureNamegtMEASUR
E_1lt/MeasureNamegt   ltMeasureMethodgtFIRST_METHO
Dlt/MeasureMethodgt   ltMeasureMethodParametersgt1
20 0.5 30lt/MeasureMethodParametersgt  
ltMeasureValuegt0.73lt/MeasureValuegt  
lt/Measuregt ltMeasuregt   ltMeasureNamegtMEASURE
_2lt/MeasureNamegt   ltMeasureMethodgtSECOND_METHO
Dlt/MeasureMethodgt   ltMeasureMethodParametersgt6
0 0.75lt/MeasureMethodParametersgt  
ltMeasureValuegt1.24lt/MeasureValuegt  
lt/Measuregt lt/Wellgt lt!-- other wells here  
--gt lt/Plategt
Added
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How to Simplify and Speed up the Adoption of the
Proposed SBS Image and Data Exchange Standard for
HCS/HCA

1. Form a permanent SBS Committee to work out
   technical details.
2. Provide free and open source SW to read, write,
   and convert to and from other formats the
   proposed XML files of HCS/HCA data.
3. Provide validation data sets in this format, e.g.
   SBS Image Library for algorithm comparison.

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How the Standard Can Change the Business Model
for Software Development in HCS/HCA

1. A biological research group post images,
   description, and design goals for a new assay
   (e.g., statistical quality, speed of processing,
   cost, minimal required number of cells) and
   relevant restrictions (e.g., type of
   computer/operating system) and business terms
   (e.g., needed number of licenses)
2. Interested image analysis developers compete on
   this problem and return their results (privately
   or publicly).
3. The research group compares results, possibly
   runs more detailed tests and makes a decision.
   Both groups sign a contract.