Imaging preparation protocol

Expansion factorimaging_preparation_protocol.expansion_factor (number) Factor by which the imaged tissue was expanded in one dimension. For example "3".

Fiducial markerimaging_preparation_protocol.fiducial_marker (string) Fiducial markers for the alignment of images taken across multiple rounds of imaging. For example "beads".

Final slicing methodimaging_preparation_protocol.final_slicing_method (string) The method by which the final slice was obtained. For example "cryosectioning".

Fresh slicing methodimaging_preparation_protocol.fresh_slicing_method (string) The method by which fresh tissue was sliced. For example "vibrotome".

Imaged slice thicknessimaging_preparation_protocol.imaged_slice_thickness (number) Thickness of the imaged slice in micrometres. For example "10".

Permeabilisation timeimaging_preparation_protocol.permeabilisation_time (number) The permeabilisation time in time units that the tissue was exposed to. For example "12".

Post final slicing intervalimaging_preparation_protocol.post_final_slicing_interval (number) Length of time between secondary slicing and hybridization. For example "7".

Time between resection and fresh slicingimaging_preparation_protocol.post_resection_interval (number) Length of time between surgical resection and fresh slicing of tissue. For example "5".

Imaging preparation protocol>Permeabilisation time unit (time_unit_ontology object) The unit in which permeabilisation time is expressed.

Time unit ontology IDimaging_preparation_protocol.permeabilisation_time_unit.ontology (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.

Time unit ontology labelimaging_preparation_protocol.permeabilisation_time_unit.ontology_label (string from time_unit_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 "second" or "week".

Time unitRequiredimaging_preparation_protocol.permeabilisation_time_unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

Imaging preparation protocol>Post final slicing interval time unit (time_unit_ontology object) The unit of time in which the post final slicing interval is expressed. For example "day".

Time unit ontology IDimaging_preparation_protocol.post_final_slicing_interval_unit.ontology (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.

Time unit ontology labelimaging_preparation_protocol.post_final_slicing_interval_unit.ontology_label (string from time_unit_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 "second" or "week".

Time unitRequiredimaging_preparation_protocol.post_final_slicing_interval_unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

Imaging preparation protocol>Post resection interval time unit (time_unit_ontology object) The unit of time in which the post resection interval is expressed. For example "day".

Time unit ontology IDimaging_preparation_protocol.post_resection_interval_unit.ontology (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.

Time unit ontology labelimaging_preparation_protocol.post_resection_interval_unit.ontology_label (string from time_unit_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 "second" or "week".

Time unitRequiredimaging_preparation_protocol.post_resection_interval_unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

Imaging preparation protocol>Pre-final slice preservation method (preservation_storage object) Tissue preservation method used prior to final slicing. For example "freezing".

Preservation methodimaging_preparation_protocol.pre_final_slice_preservation_method.preservation_method (string enum from preservation_storage) The method by which a biomaterial was preserved through the use of chemicals, cold, or other means to prevent or retard biological or physical deterioration. Should be one of: "cryopreservation in liquid nitrogen (dead tissue)", "cryopreservation in dry ice (dead tissue)", "cryopreservation of live cells in liquid nitrogen", "cryopreservation, other", "formalin fixed, unbuffered", "formalin fixed, buffered", "formalin fixed and paraffin embedded", "hypothermic preservation media at 2-8C" or "fresh".

Storage methodimaging_preparation_protocol.pre_final_slice_preservation_method.storage_method (string enum from preservation_storage) The method by which a biomaterial was stored after preservation or before another protocol was used. Should be one of: "ambient temperature", "cut slide", "fresh", "frozen at -70C", "frozen at -80C", "frozen at -150C", "frozen in liquid nitrogen", "frozen in vapor phase", "paraffin block", "RNAlater at 4C", "RNAlater at 25C" or "RNAlater at -20C".

Storage timeimaging_preparation_protocol.pre_final_slice_preservation_method.storage_time (number from preservation_storage) Length of time the biomaterial was stored for in Storage time units. For example "5".

Imaging preparation protocol>Pre-final slice preservation method>Storage time unit (time_unit_ontology object) The unit in which Storage time is expressed.

Time unit ontology IDimaging_preparation_protocol.pre_final_slice_preservation_method.storage_time_unit.ontology (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.

Time unit ontology labelimaging_preparation_protocol.pre_final_slice_preservation_method.storage_time_unit.ontology_label (string from time_unit_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 "second" or "week".

Time unitRequiredimaging_preparation_protocol.pre_final_slice_preservation_method.storage_time_unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

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

Document filenameimaging_preparation_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_preparation_protocol.protocol_core.protocol_description (string from protocol_core) A general description of the protocol.

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

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

protocols.io DOIimaging_preparation_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_preparation_protocol.protocol_core.publication_doi (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".

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

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

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

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

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

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

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

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

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