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Minimum Information for High Content Analysis

(MIAHA)

Mark Collins Ph.D

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Background

Drive towards a standard for HCS data interchange• More than just the image• Meta data

Cellomics (now ThermoFisher) has developed a set of Minimum Information guidelines for exchange of data between HCS platforms

• NOT a standard Walk through the minimum information

• Solicit input Hand this over to an independent body to create the standard

• Vendor neutral

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What is Minimum Information?

Purpose• To establish criteria by which HCS/HCA experiments may be

recorded that provides enough detail to allow for correct interpretation and interchange of data

• NOT software, not XML, not code libraries• These may come later

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Why Minimum Information for HCS?

•Variety of imagers,•Image analysis software•Data management•Data analysis

•Desire for ‘open’ access, best tools for task

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Standards drive innovationMultiple consumers and providers of information

HCSData

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Image analysis

Data mining

Data visualization

Data management

Modelling

simulation

Acquisition

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Minimum Information for High Content Analysis

Five basic elements• Experiment• Sample Details• Campaign• Instrument• Data

• Multiple elements Use clear ontologies

IMPORTANT

•it’s the MINIMUM Information (MInf) to allow interpretation

•NOT a complete data model

•NOT a schema or file spec

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A word on Ontologies

Key to MInf• Consistent vocabulary for descriptive elements (e.g cell types etc)

MIAHA will use• Ontology for Biomedical Investigation (OBI)• FuGO (Functional Genomics Ontology)• MeSH (medical subject headings – NLM)• SNOMED• NCBI Taxonomy

We may agree our own terminology for HCA• Cellomics has such an ontology we will share

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Ontology for HCA - excerpt

Dilution: The process of adding solvent to a test substance. Specified as the proportion of the sample volume in the final volume. For example, adding 9 micro liters of water to 1 micro liter of an anisomycin solution (of any concentration) represents a dilution of 1:10. Display Setting: User-specified value that controls how the images and data generated by the image analysis algorithms are displayed, but has no effect on the operation of the algorithms. Dose Response: A means of determining if a the activity of a test substance is related to its concentration. Usually there is a direct relationship with increasing dilution (decreasing concentration) and activity. EC50: The concentration of an agonist which produces 50% of the maximum possible response for that agonist. Entity: An entity is one of the following: Plate, Scan, Well, Pass, Field, or Object. Entities are what measurements are taken on, and annotations associated with. Entities are instances of nodes. Event: An obsolete term from the ArrayScan Software. Refers to a combination of responses. This term has been replaced by Hit. Exporting: A process that copies the files and/or relational data associated with a scan from a central store to a client computer. Alternately: The act of transferring a protocol, form factor, or other resource to a file that can later be imported. Extents: An obsolete term from the ArrayScan Software. Refers to well level reference levels. Feature: An obsolete term from the ArrayScan Software. Feature has been replaced with measurement. Field: A field is a set of one or more images of a single sub-region within a well, acquired as one or more channels, representing the field of view of the camera in each channel. Field Image: An image of a single field (containing one or more channels). Field of View: See Field. Field Time: The time, in real time, that a field image is captured. Fixed End Point Experiment: An experiment which consists of a single-pass analysis of Fixed-Cell cellular objects. Fixed-Cell: An experiment in which the user observes the properties of cellular objects after they have reached their targeted state by fixing (killing) the cells at a particular time. This is the opposite of a Live-Cell experiment. Fluorescence Microscopy: A detection technique that is used to measure the fluorescence of a label.

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The major elements of MIAHA

Walk through the major elements of MIAHA Open for discussion Independent body should draft the MIAHA requirements

• We will hand over work so far

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Element: Experiment MIAHA defines that the following pieces of information shall be provided for the basic element

Name Abstract

• Brief description of the experiment, purpose, rationale etc Keywords

• Ontology based keywords, e.g. Kinase, IL-1 Experiment variables

• Brief description of the variables that are being assessed, e.g. EGF treatment vs.control

Project• Name• Description• Owner

Experimenter• Name• Address• URL• Email Address• Organization

Date

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Element: Sample Details MIAHA defines that the following pieces of information shall be provided for the basic element

Description of each sample (test, reagent, cell-line etc) used in the Experiment

Sample Type Sample Description Sample Source Sample Characteristics

• Chemical structure, SDF, MOL etc Sample External Information

• CAS, Genbank ID etc, ATCC Sample Treatment Fluorescent Reagent

• Characteristics• Analyte• Detection• Manufacturer name• Catalog number

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Element: Campaign (a.k.a Screen) MIAHA defines that the following pieces of information shall be provided for the basic element

Describes a collection of experiments with a common theme over multiple runs or batches of samples & plates

Name Description Project Creation Date End Date

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Element: Instrument MIAHA defines that the following pieces of information shall be provided for the basic element

Describes the instrument used to acquire the image (adapted from OME)

Manufacturer Model Number Catalog number Microscope Light source Detector Objective Filter

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Element: Data MIAHA defines that the following pieces of information shall be provided for the basic element

Defines all data related to the other elements, each Data element has a Specification associated with it.

Image ScanData Plate Data Annotation Data Protocol Data Measure Well Data Pass Data Field Data Channel Data Object Data

We’ll go into detail on just 4 of these

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Element: Image MIAHA defines that the following pieces of information shall be provided for the basic element

Defines the information about an image (adapted from OME)

ChannelInfo Col Row Field Pass ZIndex FileType Format Headersize Height Width ImageSource PixelSizeX PixelSizeY PixelSizeZ

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Element: Plate MIAHA defines that the following pieces of information shall be provided for the basic element

Defines the information for a plate (or container) that ‘holds’ images (adapted from OME)

Identifier Barcode Name FormFactor Manufacturer Catalog number Number of Rows Number of Columns ProjectRef

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Element: Measure MIAHA defines that the following pieces of information shall be provided for the basic element

Defines any numerical or categorical variables generated as a result of an analysis (image or other)

Name Description Value Method Limits Attributes

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Element: Object MIAHA defines that the following pieces of information shall be provided for the basic element

Defines the data to describe an object in an image

Identifier Measures Type

• Cell• Colony• SubCell• Spot

Overlays/Masks

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Next Steps

MIAHA is just a ‘straw man’, NOT a standard• Defined the Minimum Information

Pass to an independent body• Write a MInf specification document• Post for comment• Develop a standard from this

Once posted• Develop software, file specs etc

Will require resources• Thermo Fisher will contribute to a fund for the standards creation

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Validating MIAHA

Webservices API implements the MIAHA idea

Uses WCF Number of test ‘consumers’

• C#• Excel2007• MatLab

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Excel2007 Consumer of HCS MIAHA data

Excel loads HCS data via the web service

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Validating MIAHA

Search for the data of interest

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Validating MIAHA

Display the data in Excel