Specimen types
Type-specific details of individual specimens: one slice, section, well or organoid of a set.
Table of contents
Culture item
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.
| Field | Description |
|---|---|
Cell line | Text. Cell line or primary preparation this item is made of, as a short label. |
Container type | Choice. Kind of vessel this item is held in. Options: Dish, Flask, Multiwell plate, Coverslip, Membrane insert, Chamber slide, Microfluidic chip, Gel dome, Tube, Cryovial, Other. |
Container ID | Text. Label on this item’s own dish, flask, coverslip or tube. |
Passages since establishment | Integer. Passages since its culture was established (not counting the source material’s passage), as of when this item was seeded. Range: ≥ 0. |
Population doublings | Number. Cumulative population doublings since its culture was established (not counting earlier ones), as of when this item was seeded. Range: ≥ 0. |
Condition | Text. Experimental arm this item belongs to, as a short label. |
Organoid
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.
| Field | Description |
|---|---|
Cell line | Text. Cell line or primary preparation this organoid came from, as a short label. |
Container ID | Text. Label on this organoid’s own well, tube or vial; empty while it shares a dish. |
Other
Represents an item of a specimen set when no other specimen type fits, described by a short label and its container ID.
| Field | Description |
|---|---|
Item type | Text. What this item is, as a short label, when no other specimen type fits. |
Container ID | Text. Label on this item’s own tube, vial or slide. |
Section
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.
| Field | Description |
|---|---|
Cut order | Integer. Place of this section in the cutting order off the block, counting sections that were discarded. Range: ≥ 1. |
Thickness | Quantity with unit. Thickness this section was cut at, where it differs from the nominal thickness of its series. Units: nm, µm, mm, m. |
Relative position | Quantity with unit. Position of this section along the series’ coordinate axis, measured from the series’ coordinate origin. Units: nm, µm, mm, m. |
Position provenance | Choice. How this section’s relative position was obtained. Options: Derived from cut order and thickness, Atlas registration, Landmark measurement, Other. |
Container ID | Text. Label on this section’s own slide, tube or well. |
Slide position | Integer. Position of this section on its slide, counted from the label end; 1 is the section nearest the label. Range: ≥ 1. |
Slice
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.
| Field | Description |
|---|---|
Cut order | Integer. Place of this slice in the cutting order off the block, counting slices that were discarded. Range: ≥ 1. |
Thickness | Quantity with unit. Thickness this slice was cut at, where it differs from the nominal thickness of its series. Units: nm, µm, mm, m. |
Relative position | Quantity with unit. Position of this slice along the series’ coordinate axis, measured from the series’ coordinate origin. Units: nm, µm, mm, m. |
Container ID | Text. Label on this slice’s own well, tube or vial; empty while it shares a chamber. |
Tissue piece
Represents a discrete piece of tissue, such as a dissected region or biopsy, with its type, largest dimension, mass and container label.
| Field | Description |
|---|---|
Item type | Text. Short label for what kind of tissue piece this is. |
Largest dimension | Quantity with unit. Length of this piece along its longest axis, as measured when it was recorded. Units: nm, µm, mm, m. |
Mass | Quantity with unit. Mass of this piece as weighed when it was recorded. Units: kg, g, mg, µg, ng. |
Container ID | Text. Label on this piece’s own jar, vial, tube or cassette. |
Well
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.
| Field | Description |
|---|---|
Well | Text. Address on the plate, row letters then column number; A1 is the top-left well. |
Cell line | Text. Cell line or primary preparation growing in this well, as a short label. |
Condition | Text. Experimental arm this well belongs to, as a short label. |
Sample role | Choice. What this well is for in the plate design. Options: Unknown sample, Standard, Positive control, Negative control, Vehicle control, Untreated control, Blank, Reference compound, Other. |
Exclusion reason | Choice. Why this well was excluded from analysis; left empty when it was kept. Options: Contamination (bacterial, fungal or mycoplasma), Edge evaporation, Seeding failure, Cells detached, Dispensing error, Operator error, Failed quality control, Not used, Other. |
API access
The same types are documented for API users, with property codes, versions and payload examples, on the Specimen schemas API page.