Imaging Protocol

Refractive index of the immersion mediumimaging_protocol.immersion_medium_refractive_index (number) Refractive index of the immersion medium used for imaging. For example "1.5" or "1".

Immersion mediumimaging_protocol.immersion_medium_type (string) Immersion medium used for imaging. For example "oil" or "air".

MagnificationRequiredimaging_protocol.magnification (string) Magnification of the objective used for imaging. For example "60x" or "100x".

Microscope setup descriptionimaging_protocol.microscope_setup_description (string) Description of the microscope setup. For example "Motorized stage (SCAN IM 112 x 74, Marzhauser), sCMOS camera (Zyla 4.2", "Andor), 60x, Plan-Apo, 1.3 NA, silicone oil objective (UPLSAPO60XS2" or "Olympus).".

Number of tilesimaging_protocol.number_of_tiles (integer) Number of XY tiles in the experiment. For example "2000".

Number of Z stepsimaging_protocol.number_of_z_steps (integer) Number of steps in a Z stack. For example "40".

Numerical apertureimaging_protocol.numerical_aperture (number) Numerical aperture of the objective. For example "1.3" or "0.75".

Overlapping tilesimaging_protocol.overlapping_tiles (string enum) Whether tiles were collected with overlap. Should be one of: "yes" or "no".

Pixel sizeimaging_protocol.pixel_size (number) Pixel size in nanometers. For example "109".

Tile size Ximaging_protocol.tile_size_x (number) X size of the tile in micrometers. For example "100".

Tile size Yimaging_protocol.tile_size_y (number) Y size of the tile in micrometers. For example "100".

Z stack step sizeimaging_protocol.z_stack_step_size (number) Z-stack step size in nanometers. For example "200".

Imaging Protocol>Channel (channel array) Information about each channel used in the imaging protocol.

Channel IDRequiredimaging_protocol.channel.channel_id (string from channel) User given ID. If there is an accompanying codebook, this name should correspond to the channel id used in the codebook. For example "1" or "A".

Excitation wavelengthRequiredimaging_protocol.channel.excitation_wavelength (number from channel) Excitation wavelength of the lightsource in nanometers. For example "640".

Exposure timeRequiredimaging_protocol.channel.exposure_time (number from channel) Acquisition time for a single image per channel, in milliseconds. For example "400".

Filter rangeRequiredimaging_protocol.channel.filter_range (string from channel) Emission filter in nanometers. For example "461/70".

Multiplexed experimentRequiredimaging_protocol.channel.multiplexed (string enum from channel) Whether multiple targets were detected simultaneously in this channel. Should be one of: "yes" or "no".

Target fluorophoreimaging_protocol.channel.target_fluorophore (string from channel) The name of the fluorophore this channel is designed to assay. For example "Alexa 647".

Imaging Protocol>Microscopy techniqueRequired (microscopy_ontology object) The type of microscopy.

Microscopy ontology IDimaging_protocol.microscopy_technique.ontology (string from microscopy_ontology) An ontology term identifier in the form prefix:accession. For example "FBbi:00000251" or "FBbi:00000246".Graph restriction: Subclasses of FBbi:00000241 from obo:hcao or obo:fbbi.

Microscopy ontology labelimaging_protocol.microscopy_technique.ontology_label (string from microscopy_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "confocal microscopy" or "fluorescence microscopy".

MicroscopyRequiredimaging_protocol.microscopy_technique.text (string from microscopy_ontology) The name of the type of microscopy used in an imaging experiment. For example "confocal microscopy" or "fluorescence microscopy".

Imaging Protocol>Probe (probe array) Information about each probe in the imaging experiment.

Channelimaging_protocol.probe.channel_label (array from probe) Channel label used to assay signal. For example "1" or "A".

Fluorophoreimaging_protocol.probe.fluorophore (array from probe) Fluorophore used to detect target. For example "Cy5" or "Alexa 488".

Probe labelRequiredimaging_protocol.probe.probe_label (string from probe) The label of a probe used to detect target in this experiment. For example "ACTA1" or "cFos".

Probe sequenceimaging_protocol.probe.probe_sequence (string from probe) Sequence of a probe used to detect target. For example "AGGCTATAGCGGAGCTACG" or "aggctatagcggagctacg".

Target label in codebookimaging_protocol.probe.target_codebook_label (string from probe) A label used in the codebook for the target. For example "AKT1" or "CFOS".

Target labelRequiredimaging_protocol.probe.target_label (string from probe) An identifier for the target molecule. For example "CHEBI:85345" or "ENSG00000170345".

Target nameimaging_protocol.probe.target_name (string from probe) The name of the target molecule. For example "ACTA1_exon1" or "nuclear cFos".

Imaging Protocol>Probe>Assay typeRequired (process_type_ontology object) Type of assay used to detect target. For example "MERFISH" or "in situ sequencing".

Process type ontology IDimaging_protocol.probe.assay_type.ontology (string from process_type_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0009128" or "EFO:0009121".Graph restriction: Subclasses of EFO:0002694 from obo:efo.

Process type ontology labelimaging_protocol.probe.assay_type.ontology_label (string from process_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "enzymatic dissociation" or "blood draw".

Process typeRequiredimaging_protocol.probe.assay_type.text (string from process_type_ontology) The name of a process type being used. For example "enzymatic dissociation" or "blood draw".

Imaging Protocol>Probe>Probe construction reagents (purchased_reagents object) Name of reagents used to construct the probe.

Catalog numberimaging_protocol.probe.probe_reagents.catalog_number (string from purchased_reagents) The catalog number of the kit/reagent. For example "20014279".

Expiry dateimaging_protocol.probe.probe_reagents.expiry_date (string from purchased_reagents) The date of expiration for the kit/reagent. For example "2018-01-31" or "2018-01".

Titerimaging_protocol.probe.probe_reagents.kit_titer (string from purchased_reagents) Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. For example "3.0x10^7".

Batch/lot numberimaging_protocol.probe.probe_reagents.lot_number (string from purchased_reagents) The batch or lot number of the kit/reagent. For example "10001A".

Manufacturerimaging_protocol.probe.probe_reagents.manufacturer (string from purchased_reagents) The manufacturer of the kit/reagent. For example "Illumina" or "ThermoFisher Scientific".

Retail nameimaging_protocol.probe.probe_reagents.retail_name (string from purchased_reagents) The retail name of the kit/reagent. For example "SureCell WTA 3' Library Prep Kit" or "CytoTune iPS 2.0 Sendai Reprogramming Kit".

Imaging Protocol>Probe>Target subcellular structure (cellular_component_ontology object) Target subcellular structure.

Subcellular structure ontology IDimaging_protocol.probe.subcellular_structure.ontology (string from cellular_component_ontology) An ontology term identifier in the form prefix:accession. For example "GO:0005737" or "GO:0005634".Graph restriction: Subclasses of GO:0005575 from obo:hcao or obo:go.

Subcellular structure ontology labelimaging_protocol.probe.subcellular_structure.ontology_label (string from cellular_component_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "cytoplasm" or "nucleus".

Subcellular structureRequiredimaging_protocol.probe.subcellular_structure.text (string from cellular_component_ontology) The name of a subcellular structure. For example "cytoplasm" or "nucleus".

Imaging Protocol>Protocol coreRequired (protocol_core object) Core protocol-level information.

Document filenameimaging_protocol.protocol_core.document (string from protocol_core) A filename of a PDF document containing the details of the protocol. For example "my_cool_protocol.pdf".

Protocol descriptionimaging_protocol.protocol_core.protocol_description (string from protocol_core) A general description of the protocol.

Protocol IDRequiredimaging_protocol.protocol_core.protocol_id (string from protocol_core) A unique ID for the protocol.

Protocol nameimaging_protocol.protocol_core.protocol_name (string from protocol_core) A short name for the protocol.

protocols.io DOIimaging_protocol.protocol_core.protocols_io_doi (string from protocol_core) The protocols.io digital object identifier (doi) for the protocol. For example "10.17504/protocols.io.mgjc3un".

Publication DOIimaging_protocol.protocol_core.publication_doi (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".

Imaging Protocol>provenance (provenance object) Provenance information provided by the system.

Accessionimaging_protocol.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredimaging_protocol.provenance.document_id (string from provenance) Identifier for document.

Schema major versionimaging_protocol.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versionimaging_protocol.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredimaging_protocol.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDimaging_protocol.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update dateimaging_protocol.provenance.update_date (string from provenance) When project was last updated.

Updater IDimaging_protocol.provenance.updater_id (string from provenance) ID of individual who last updated project.