Specimen set types

Type-specific details of specimen sets: tissue or cultures prepared together.

Additional fields
Culture
Organoid batch
Other
Section series
Slice series
Well plate
Whole tissue
API access

Additional fields

Any extra parameters you want to add to this specimen set. Saved as key-value pairs. Values can be strings or numbers.

Field	Description
`key`	Text.
`value`	Object.

Culture

Describes a culture of cells or tissue, such as organotypic slices on inserts, with how it was established, format, day 0 event, growth surface and coating, medium, incubator settings and termination reason.

Field	Description
`Culture preparation`	Choice. How the cultured material was obtained and prepared when the culture was established. Options: Primary dissociated, Primary explant, Organotypic slice, Immortalized cell line, Stem-cell-derived, Other.
`Culture format`	Choice. Physical format the culture is currently held in. Options: Submerged, Static suspension, Orbital shaker, Spinning bioreactor, Roller tube, Microwell array, Air-liquid interface, Perfused, Other.
`Day 0 event`	Choice. Event the culture’s day count is reckoned from (day 0). Options: Dissection, Dissociation or plating, Sectioning, Thaw, Aggregate formation, Neural induction, Matrix embedding, Other.
`Passage at establishment`	Integer. Passage number of the source material when this culture was established, as labelled on the vial or bank record; empty for primary cultures. Range: ≥ 0.
`Specimens per vessel`	Integer. Nominal number of specimens in each dish, well or insert (e.g., 3 slices per insert). Range: ≥ 1.
`Growth surface`	Text. Surface or support the culture grows on, without its coating.
`Coating`	Multi-select. Coatings applied to the growth surface; select every one used. Options: None (uncoated), Poly-L-lysine, Poly-D-lysine, Poly-ornithine, Laminin, Fibronectin, Collagen I, Collagen IV, Gelatin, Vitronectin, Basement membrane matrix, Other.
`Medium`	Text. Medium the culture is kept in, as prepared, recorded as a single label.
`Incubation temperature`	Quantity with unit. Incubator temperature the culture is kept at, as set rather than as measured. Units: °C, K.
`CO₂ level`	Quantity with unit. CO₂ level of the incubator atmosphere, as set rather than as measured. Units: % v/v, ppm.
`O₂ level`	Quantity with unit. O₂ level of the incubator atmosphere, as set rather than as measured; not dissolved oxygen. Units: % v/v, ppm.
`Humidification`	Choice. How the incubator atmosphere is humidified, as set. Options: Humidified, Actively humidity-controlled, Deliberately dry.
`Termination reason`	Choice. Why the culture ended, recorded when it was terminated. Options: Used up, Bacterial or fungal contamination, Mycoplasma contamination, Failed to establish, Poor health, Planned endpoint reached, Storage or equipment failure, Other.

Organoid batch

Describes a production run of organoids, which may span several vessels, with batch ID, day 0 event, differentiation protocol type, culture format, agitation, medium and incubator settings.

Field	Description
`Batch ID`	Text. The lab’s code for this production run, which may span several vessels.
`Day 0 event`	Choice. Event the batch’s day count is reckoned from (day 0). Options: Dissection, Dissociation or plating, Sectioning, Thaw, Aggregate formation, Neural induction, Matrix embedding, Other.
`Guidance mode`	Choice. Kind of differentiation protocol the run follows. Options: Unguided, Guided (region-patterned).
`Culture format`	Choice. Physical culture format currently in effect for the batch. Options: Submerged, Static suspension, Orbital shaker, Spinning bioreactor, Roller tube, Microwell array, Air-liquid interface, Perfused, Other.
`Agitation rate`	Quantity with unit. Rotational speed the batch is agitated at, as set on the shaker or bioreactor. Units: RPM, Hz.
`Medium`	Text. Medium the batch is declared to be kept in, as prepared, recorded as a single label.
`Incubation temperature`	Quantity with unit. Incubator temperature the batch is kept at, as set rather than as measured. Units: °C, K.
`CO₂ level`	Quantity with unit. CO₂ level of the incubator atmosphere, as set rather than as measured. Units: % v/v, ppm.
`Humidification`	Choice. How the incubator atmosphere is humidified, as set. Options: Humidified, Actively humidity-controlled, Deliberately dry.

Other

Describes a set of ex-vivo material that none of the other specimen set types fits.

This type has no type-specific fields. The record’s own fields and its material rows describe it.

Section series

Describes a series of sections cut from the same tissue, with cutting plane, the axis and origin used to position sections, default thickness, sections per slide and the slide box or plate holding the series.

Field	Description
`Orientation`	Text. Anatomical plane in which the sections of this series were cut; for an oblique cut, state the plane it deviates from.
`Coordinate axis`	Text. Axis along which section positions in this series are indexed and measured.
`Coordinate origin`	Text. Landmark from which section positions in this series are measured.
`Default thickness`	Quantity with unit. Nominal thickness of the sections in this series; a section’s own thickness overrides it. Units: nm, µm, mm, m.
`Sections per slide`	Integer. Nominal number of sections mounted on each slide of this series; the last slide may hold fewer. Range: ≥ 1.
`Container ID`	Text. Label on the one slide box or plate holding the whole series; empty when the series spans several carriers.

Slice series

Describes a series of living slices, such as acute brain slices, with cutting plane, the axis and origin used to position slices, default thickness and the holding solution.

Field	Description
`Orientation`	Text. Anatomical or preparation plane in which the slices of this series were cut; for an oblique cut, state the plane it deviates from.
`Coordinate axis`	Text. Axis along which slice positions in this series are indexed and measured.
`Coordinate origin`	Text. Landmark from which slice positions in this series are measured.
`Default thickness`	Quantity with unit. Nominal slice thickness declared for this series; a slice’s own recorded thickness overrides it. Units: nm, µm, mm, m.
`Holding solution`	Text. Solution the living slices were declared to be held in between cutting and use.

Well plate

Describes a multi-well plate or chambered slide, with its label, format, edge-well handling, coating and incubator settings. Individual wells are recorded as Well specimens.

Field	Description
`Container ID`	Text. Label or barcode on the plate itself, as written on the lid or read by a scanner.
`Plate format`	Choice. Number of wells on the plate or chambered slide. Options: 1-well, 2-well, 4-well, 6-well, 8-well, 12-well, 24-well, 48-well, 96-well, 384-well, 1536-well, Other.
`Edge-well policy`	Choice. How the plate’s outer ring of wells was handled. Options: Used for samples, Filled with buffer or medium, Left empty, Seeded, excluded from analysis, Other.
`Coating`	Multi-select. Coating on the wells’ growth surface; select every layer applied. Options: None (uncoated), Poly-L-lysine, Poly-D-lysine, Poly-ornithine, Laminin, Fibronectin, Collagen I, Collagen IV, Gelatin, Vitronectin, Basement membrane matrix, Other.
`Incubation temperature`	Quantity with unit. Temperature the plate was kept at, as set on the incubator rather than as measured. Units: °C, K.
`CO₂ level`	Quantity with unit. CO₂ level of the incubator atmosphere the plate was kept in, as set rather than as measured. Units: % v/v, ppm.
`Humidification`	Choice. How the incubator atmosphere was humidified, as set. Options: Humidified, Actively humidity-controlled, Deliberately dry.

Whole tissue

Describes an intact tissue or organ kept whole, such as an extracted brain, with the label of its container when held in one.

Field	Description
`Container ID`	Text. Label on the one jar, vial or bag holding all of this tissue; empty when the tissue is split across several containers.

API access

The same types are documented for API users, with property codes, versions and payload examples, on the SpecimenSet schemas API page.