Specimen schemas

Type-specific details of individual specimens: one slice, section, well or organoid of a set.

Table of contents

1. How to use this family
2. Quick type map
3. Culture item
4. Organoid
5. Other
6. Section
7. Slice
8. Tissue piece
9. Well

How to use this family

• specimen: set type to a type code below and send its properties in details.
• Every version is published at https://www.brainstem.org/schemas/Specimen/<Type>/<version>.json and never changes; https://www.brainstem.org/schemas/Specimen/<Type>.json is the current version and https://www.brainstem.org/schemas/Specimen/<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
CultureItem	Culture item	2.0.0	none	2.0.0.json
Organoid	Organoid	2.0.0	none	2.0.0.json
Other	Other	2.0.0	none	2.0.0.json
Section	Section	2.0.0	none	2.0.0.json
Slice	Slice	2.0.0	none	2.0.0.json
TissuePiece	Tissue piece	2.0.0	none	2.0.0.json
Well	Well	2.0.0	none	2.0.0.json

Culture item

• type code CultureItem · version 2.0.0 · schema

Represents a single vessel or coverslip of a culture, such as a dish, flask or tube, with cell line, container, passage and population doubling counts, and experimental condition.

Property	Title	Shape	Required	Allowed values	Meaning
cellLine	Cell line	text			Cell line or primary preparation this item is made of, as a short label.
containerType	Container type	choice		one of dish, flask, multiwell_plate, coverslip, membrane_insert, chamber_slide, microfluidic_chip, gel_dome, tube, cryovial, other	Kind of vessel this item is held in.
containerId	Container ID	text			Label on this item’s own dish, flask, coverslip or tube.
passage	Passages since establishment	integer		≥ 0	Passages since its culture was established (not counting the source material’s passage), as of when this item was seeded.
populationDoublings	Population doublings	number		≥ 0	Cumulative population doublings since its culture was established (not counting earlier ones), as of when this item was seeded.
condition	Condition	text			Experimental arm this item belongs to, as a short label.

Illustrative payload:

{
    "cellLine": "text",
    "containerType": "dish"
}

Organoid

• type code Organoid · version 2.0.0 · schema

Represents a single organoid, with the cell line or primary preparation it came from and its own container label once it no longer shares a dish.

Property	Title	Shape	Required	Allowed values	Meaning
cellLine	Cell line	text			Cell line or primary preparation this organoid came from, as a short label.
containerId	Container ID	text			Label on this organoid’s own well, tube or vial; empty while it shares a dish.

Illustrative payload:

{
    "cellLine": "text",
    "containerId": "text"
}

• Fields hidden by the web form for this type (leave empty): laterality.

Other

• type code Other · version 2.0.0 · schema

Represents an item of a specimen set when no other specimen type fits, described by a short label and its container ID.

Property	Title	Shape	Required	Allowed values	Meaning
itemType	Item type	text			What this item is, as a short label, when no other specimen type fits.
containerId	Container ID	text			Label on this item’s own tube, vial or slide.

Illustrative payload:

{
    "itemType": "text",
    "containerId": "text"
}

Section

• type code Section · version 2.0.0 · schema

Represents a single tissue section of a section series, with its cut order, thickness where it differs from the series, position along the series axis and how it was obtained, and its slide and position on the slide.

Property	Title	Shape	Required	Allowed values	Meaning
index	Cut order	integer		≥ 1	Place of this section in the cutting order off the block, counting sections that were discarded.
thickness	Thickness	quantity with unit		units nm, µm, mm, m; default {"unit": "µm"}	Thickness this section was cut at, where it differs from the nominal thickness of its series.
relativePosition	Relative position	quantity with unit		units nm, µm, mm, m; default {"unit": "mm"}	Position of this section along the series’ coordinate axis, measured from the series’ coordinate origin.
positionProvenance	Position provenance	choice		one of derived_from_cut_order, atlas_registration, landmark_measurement, other	How this section’s relative position was obtained.
containerId	Container ID	text			Label on this section’s own slide, tube or well.
slidePosition	Slide position	integer		≥ 1	Position of this section on its slide, counted from the label end; 1 is the section nearest the label.

Illustrative payload:

{
    "index": 1,
    "thickness": {
        "value": 1,
        "unit": "µm"
    }
}

Slice

• type code Slice · version 2.0.0 · schema

Represents a single slice of a slice series, with its cut order, thickness where it differs from the series, position along the series axis and its own container.

Property	Title	Shape	Required	Allowed values	Meaning
index	Cut order	integer		≥ 1	Place of this slice in the cutting order off the block, counting slices that were discarded.
thickness	Thickness	quantity with unit		units nm, µm, mm, m; default {"unit": "µm"}	Thickness this slice was cut at, where it differs from the nominal thickness of its series.
relativePosition	Relative position	quantity with unit		units nm, µm, mm, m; default {"unit": "mm"}	Position of this slice along the series’ coordinate axis, measured from the series’ coordinate origin.
containerId	Container ID	text			Label on this slice’s own well, tube or vial; empty while it shares a chamber.

Illustrative payload:

{
    "index": 1,
    "thickness": {
        "value": 1,
        "unit": "µm"
    }
}

Tissue piece

• type code TissuePiece · version 2.0.0 · schema

Represents a discrete piece of tissue, such as a dissected region or biopsy, with its type, largest dimension, mass and container label.

Property	Title	Shape	Required	Allowed values	Meaning
itemType	Item type	text			Short label for what kind of tissue piece this is.
largestDimension	Largest dimension	quantity with unit		units nm, µm, mm, m; default {"unit": "mm"}	Length of this piece along its longest axis, as measured when it was recorded.
mass	Mass	quantity with unit		units kg, g, mg, µg, ng; default {"unit": "mg"}	Mass of this piece as weighed when it was recorded.
containerId	Container ID	text			Label on this piece’s own jar, vial, tube or cassette.

Illustrative payload:

{
    "itemType": "text",
    "largestDimension": {
        "value": 1,
        "unit": "mm"
    }
}

Well

• type code Well · version 2.0.0 · schema

Represents a single well of a well plate, with its plate address, cell line, experimental condition, role in the plate design and any reason for exclusion from analysis.

Property	Title	Shape	Required	Allowed values	Meaning
well	Well	text			Address on the plate, row letters then column number; A1 is the top-left well.
cellLine	Cell line	text			Cell line or primary preparation growing in this well, as a short label.
condition	Condition	text			Experimental arm this well belongs to, as a short label.
sampleRole	Sample role	choice		one of unknown_sample, standard, positive_control, negative_control, vehicle_control, untreated_control, blank, reference_compound, other	What this well is for in the plate design.
exclusionReason	Exclusion reason	choice		one of contamination, edge_evaporation, seeding_failure, detachment, dispensing_error, operator_error, failed_quality_control, not_used, other	Why this well was excluded from analysis; left empty when it was kept.

Illustrative payload:

{
    "well": "text",
    "cellLine": "text"
}

• Fields hidden by the web form for this type (leave empty): laterality.