SpecimenSet schemas

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

Table of contents

1. How to use this family
2. Quick type map
3. Additional fields
4. Culture
5. Organoid batch
6. Other
7. Section series
8. Slice series
9. Well plate
10. Whole tissue

How to use this family

• specimenset: set type to a type code below and send its properties in details.
• Every version is published at https://www.brainstem.org/schemas/SpecimenSet/<Type>/<version>.json and never changes; https://www.brainstem.org/schemas/SpecimenSet/<Type>.json is the current version and https://www.brainstem.org/schemas/SpecimenSet/<Type>/ lists the versions. See Public schemas.
• Quantities are objects {"value": <number>, "unit": "<code>"}. Property paths with [] are inside a repeatable list of rows. The server sets the schema version field itself.

Quick type map

Type code	Title	Version	Required properties	Schema
Array	Additional fields (form only)	1.0.1	none	1.0.1.json
Culture	Culture	1.0.1	none	1.0.1.json
OrganoidBatch	Organoid batch	1.0.1	none	1.0.1.json
Other	Other	1.0.1	none	1.0.1.json
SectionSeries	Section series	1.1.1	none	1.1.1.json
SliceSeries	Slice series	1.1.1	none	1.1.1.json
WellPlate	Well plate	1.0.1	none	1.0.1.json
WholeTissue	Whole tissue	1.1.1	none	1.1.1.json

Additional fields

• type code Array · version 1.0.1 · schema

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

Property	Title	Shape	Required	Allowed values	Meaning
key	key	text
value	value	object

Illustrative payload:

[
    {
        "key": "text",
        "value": {}
    }
]

Culture

• type code Culture · version 1.0.1 · schema

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.

Property	Title	Shape	Required	Allowed values	Meaning
culturePreparation	Culture preparation	choice		one of primary_dissociated, primary_explant, organotypic_slice, immortalized_line, stem_cell_derived, other	How the cultured material was obtained and prepared when the culture was established.
cultureFormat	Culture format	choice		one of submerged, static_suspension, orbital_shaker, spinning_bioreactor, roller_tube, microwell_array, air_liquid_interface, perfused, other	Physical format the culture is currently held in.
ageReferenceEvent	Day 0 event	choice		one of dissection, dissociation_or_plating, sectioning, thaw, aggregate_formation, neural_induction, matrix_embedding, other	Event the culture’s day count is reckoned from (day 0).
passageAtEstablishment	Passage at establishment	integer		≥ 0	Passage number of the source material when this culture was established, as labelled on the vial or bank record; empty for primary cultures.
itemsPerContainer	Specimens per vessel	integer		≥ 1	Nominal number of specimens in each dish, well or insert (e.g., 3 slices per insert).
substrate	Growth surface	text			Surface or support the culture grows on, without its coating.
coating	Coating	multi-select		one of none, poly_l_lysine, poly_d_lysine, poly_ornithine, laminin, fibronectin, collagen_i, collagen_iv, gelatin, vitronectin, basement_membrane_matrix, other; format select2	Coatings applied to the growth surface; select every one used.
medium	Medium	text			Medium the culture is kept in, as prepared, recorded as a single label.
incubationTemperature	Incubation temperature	quantity with unit		units °C, K; default {"unit": "°C"}	Incubator temperature the culture is kept at, as set rather than as measured.
co2Concentration	CO₂ level	quantity with unit		units % v/v, ppm; default {"unit": "% v/v"}	CO₂ level of the incubator atmosphere, as set rather than as measured.
oxygenTension	O₂ level	quantity with unit		units % v/v, ppm; default {"unit": "% v/v"}	O₂ level of the incubator atmosphere, as set rather than as measured; not dissolved oxygen.
humidification	Humidification	choice		one of humidified, humidity_controlled, not_humidified	How the incubator atmosphere is humidified, as set.
terminationReason	Termination reason	choice		one of consumed, contamination_bacterial_or_fungal, contamination_mycoplasma, failed_to_establish, poor_health, endpoint_reached, storage_or_equipment_failure, other	Why the culture ended, recorded when it was terminated.

Illustrative payload:

{
    "culturePreparation": "primary_dissociated",
    "cultureFormat": "submerged"
}

Organoid batch

• type code OrganoidBatch · version 1.0.1 · schema

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.

Property	Title	Shape	Required	Allowed values	Meaning
batchId	Batch ID	text			The lab’s code for this production run, which may span several vessels.
ageReferenceEvent	Day 0 event	choice		one of dissection, dissociation_or_plating, sectioning, thaw, aggregate_formation, neural_induction, matrix_embedding, other	Event the batch’s day count is reckoned from (day 0).
guidanceMode	Guidance mode	choice		one of unguided, guided	Kind of differentiation protocol the run follows.
cultureFormat	Culture format	choice		one of submerged, static_suspension, orbital_shaker, spinning_bioreactor, roller_tube, microwell_array, air_liquid_interface, perfused, other	Physical culture format currently in effect for the batch.
agitationRate	Agitation rate	quantity with unit		units RPM, Hz; default {"unit": "RPM"}	Rotational speed the batch is agitated at, as set on the shaker or bioreactor.
medium	Medium	text			Medium the batch is declared to be kept in, as prepared, recorded as a single label.
incubationTemperature	Incubation temperature	quantity with unit		units °C, K; default {"unit": "°C"}	Incubator temperature the batch is kept at, as set rather than as measured.
co2Concentration	CO₂ level	quantity with unit		units % v/v, ppm; default {"unit": "% v/v"}	CO₂ level of the incubator atmosphere, as set rather than as measured.
humidification	Humidification	choice		one of humidified, humidity_controlled, not_humidified	How the incubator atmosphere is humidified, as set.

Illustrative payload:

{
    "batchId": "text",
    "ageReferenceEvent": "dissection"
}

Other

• type code Other · version 1.0.1 · schema

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

This type has no type-specific properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Section series

• type code SectionSeries · version 1.1.1 · schema

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.

Property	Title	Shape	Required	Allowed values	Meaning
orientation	Orientation	text			Anatomical plane in which the sections of this series were cut; for an oblique cut, state the plane it deviates from.
coordinateAxis	Coordinate axis	text			Axis along which section positions in this series are indexed and measured.
coordinateOrigin	Coordinate origin	text			Landmark from which section positions in this series are measured.
defaultThickness	Default thickness	quantity with unit		units nm, µm, mm, m; default {"unit": "µm"}	Nominal thickness of the sections in this series; a section’s own thickness overrides it.
itemsPerContainer	Sections per slide	integer		≥ 1	Nominal number of sections mounted on each slide of this series; the last slide may hold fewer.
containerId	Container ID	text			Label on the one slide box or plate holding the whole series; empty when the series spans several carriers.

Illustrative payload:

{
    "orientation": "text",
    "coordinateAxis": "text"
}

Slice series

• type code SliceSeries · version 1.1.1 · schema

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.

Property	Title	Shape	Required	Allowed values	Meaning
orientation	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.
coordinateAxis	Coordinate axis	text			Axis along which slice positions in this series are indexed and measured.
coordinateOrigin	Coordinate origin	text			Landmark from which slice positions in this series are measured.
defaultThickness	Default thickness	quantity with unit		units nm, µm, mm, m; default {"unit": "µm"}	Nominal slice thickness declared for this series; a slice’s own recorded thickness overrides it.
holdingSolution	Holding solution	text			Solution the living slices were declared to be held in between cutting and use.

Illustrative payload:

{
    "orientation": "text",
    "coordinateAxis": "text"
}

Well plate

• type code WellPlate · version 1.0.1 · schema

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.

Property	Title	Shape	Required	Allowed values	Meaning
containerId	Container ID	text			Label or barcode on the plate itself, as written on the lid or read by a scanner.
plateFormat	Plate format	choice		one of 1_well, 2_well, 4_well, 6_well, 8_well, 12_well, 24_well, 48_well, 96_well, 384_well, 1536_well, other	Number of wells on the plate or chambered slide.
edgeWellPolicy	Edge-well policy	choice		one of used, buffer_filled, left_empty, seeded_but_excluded, other	How the plate’s outer ring of wells was handled.
coating	Coating	multi-select		one of none, poly_l_lysine, poly_d_lysine, poly_ornithine, laminin, fibronectin, collagen_i, collagen_iv, gelatin, vitronectin, basement_membrane_matrix, other; format select2	Coating on the wells’ growth surface; select every layer applied.
incubationTemperature	Incubation temperature	quantity with unit		units °C, K; default {"unit": "°C"}	Temperature the plate was kept at, as set on the incubator rather than as measured.
co2Concentration	CO₂ level	quantity with unit		units % v/v, ppm; default {"unit": "% v/v"}	CO₂ level of the incubator atmosphere the plate was kept in, as set rather than as measured.
humidification	Humidification	choice		one of humidified, humidity_controlled, not_humidified	How the incubator atmosphere was humidified, as set.

Illustrative payload:

{
    "containerId": "text",
    "plateFormat": "1_well"
}

Whole tissue

• type code WholeTissue · version 1.1.1 · schema

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

Property	Title	Shape	Required	Allowed values	Meaning
containerId	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.

Illustrative payload:

{
    "containerId": "text"
}