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Minimum Information for High Content Analysis (MIAHA)

Minimum Information for High Content Analysis (MIAHA). Mark Collins Ph.D. Background. Drive towards a standard for HCS data interchange More than just the image Meta data

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Minimum Information for High Content Analysis (MIAHA)

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  1. Minimum Information for High Content Analysis(MIAHA) Mark Collins Ph.D

  2. 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

  3. 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

  4. Why Minimum Information for HCS? • Variety of imagers, • Image analysis software • Data management • Data analysis • Desire for ‘open’ access, best tools for task

  5. Standards drive innovationMultiple consumers and providers of information Minimum Information Data management Minimum Information Minimum Information Data visualization HCS Data Minimum Information Minimum Information Modelling Image analysis Minimum Information Data mining simulation Acquisition

  6. 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

  7. 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

  8. 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.

  9. 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

  10. Element: ExperimentMIAHA 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

  11. Element: Sample DetailsMIAHA 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

  12. 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

  13. Element: InstrumentMIAHA 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

  14. Element: DataMIAHA 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

  15. Element: ImageMIAHA 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

  16. Element: PlateMIAHA 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

  17. Element: MeasureMIAHA 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

  18. Element: ObjectMIAHA 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

  19. 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

  20. Validating MIAHA • Webservices API implements the MIAHA idea • Uses WCF • Number of test ‘consumers’ • C# • Excel2007 • MatLab

  21. Excel2007 Consumer of HCS MIAHA data • Excel loads HCS data via the web service

  22. Validating MIAHA • Search for the data of interest

  23. Validating MIAHA • Display the data in Excel

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