SpecimenLog schemas

Entry schemas for specimen logs: measurements followed over time for one specimen set.

Table of contents

1. How to use this family
2. Quick type map
3. Solution Logs
   1. Bath solution log
   2. Culture medium change
4. Environmental Logs
   1. CO₂ log
   2. Humidity log
   3. Oxygenation log
   4. pH log
   5. Temperature log
5. Health Logs
   1. Slice health log
   2. Viability assay
6. Observation Logs
   1. Generic observation

How to use this family

• specimenlog: type selects the type; each log entry added through the entry actions is validated against it.
• Every version is published at https://www.brainstem.org/schemas/SpecimenLog/<Type>/<version>.json and never changes; https://www.brainstem.org/schemas/SpecimenLog/<Type>.json is the current version and https://www.brainstem.org/schemas/SpecimenLog/<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	Group	Version	Required properties	Schema
BathSolution	Bath solution log	Solution Logs	1.0.2	none	1.0.2.json
CO2	CO₂ log	Environmental Logs	1.0.2	none	1.0.2.json
CultureMediumChange	Culture medium change	Solution Logs	1.1.2	none	1.1.2.json
GenericObservation	Generic observation	Observation Logs	1.0.0	none	1.0.0.json
Humidity	Humidity log	Environmental Logs	1.0.2	none	1.0.2.json
Oxygenation	Oxygenation log	Environmental Logs	1.0.2	none	1.0.2.json
PH	pH log	Environmental Logs	1.0.2	none	1.0.2.json
SliceHealth	Slice health log	Health Logs	1.0.2	none	1.0.2.json
Temperature	Temperature log	Environmental Logs	1.0.2	none	1.0.2.json
ViabilityAssay	Viability assay	Health Logs	1.0.2	none	1.0.2.json

Solution Logs

Bath solution log

• type code BathSolution · version 1.0.2 · schema

Logs the bath solution applied to a specimen set, such as ACSF, with exchange type, volume, temperature, pH, osmolality, perfusion flow rate, oxygenation gas and the chamber used.

Property	Title	Shape	Required	Allowed values	Meaning
solutionName	Solution name or formulation	text			Identifies the bath solution, such as ACSF or recovery solution.
exchangeType	Exchange type	choice		one of full, partial, continuous_perfusion, measurement_only	How the solution was applied or observed.
volume	Volume exchanged	quantity with unit		units µL, mL, L; default {"unit": "mL"}	The volume exchanged or added during this log event.
temperature	Solution temperature	quantity with unit		units °C, K; default {"unit": "°C"}	The solution temperature during the recorded exchange or exposure.
ph	pH	number		≥ 0 and ≤ 14	The measured pH of the bath solution.
osmolality	Osmolality	quantity with unit		units mOsm/kg; default {"unit": "mOsm/kg"}	The measured or declared osmolality of the bath solution.
flowRate	Perfusion flow rate	quantity with unit		units µL/min, mL/min, L/min; default {"unit": "mL/min"}	The perfusion flow rate during this log event.
oxygenationGas	Oxygenation gas mixture	text			Gas composition used to oxygenate the solution, for example 95% O₂ / 5% CO₂.
deviceIdentifier	Device or chamber identifier	text			The identifier of the device, chamber, or instrument used for the measurement.

Illustrative payload:

{
    "solutionName": "text",
    "exchangeType": "full"
}

Culture medium change

• type code CultureMediumChange · version 1.1.2 · schema

Logs a change of culture medium, with the replacement medium formulation, volume exchanged and any supplements added.

Property	Title	Shape	Required	Allowed values	Meaning
mediumFormulation	Medium formulation	text			The formulation or product identity of the replacement culture medium.
volume	Volume changed	quantity with unit		units µL, mL, L; default {"unit": "mL"}	The volume exchanged or added during this log event.
supplements	Supplements added	text			Supplements added to the medium during this change, including concentrations when known.

Illustrative payload:

{
    "mediumFormulation": "text",
    "volume": {
        "value": 1,
        "unit": "mL"
    }
}

Environmental Logs

CO₂ log

• type code CO2 · version 1.0.2 · schema

Logs the CO₂ concentration of the incubator atmosphere holding a culture, with the incubator ID.

Property	Title	Shape	Required	Allowed values	Meaning
co2Percent	CO₂ (%)	number		≥ 0 and ≤ 100	The carbon-dioxide concentration in the incubator atmosphere.
incubatorId	Incubator ID	text			The laboratory identifier of the incubator used for this culture.

Illustrative payload:

{
    "co2Percent": 1.0,
    "incubatorId": "text"
}

Humidity log

• type code Humidity · version 1.0.2 · schema

Logs the relative humidity of the chamber atmosphere holding a culture, with the chamber ID.

Property	Title	Shape	Required	Allowed values	Meaning
humidityPercent	Relative humidity (%)	number		≥ 0 and ≤ 100	The relative humidity of the chamber atmosphere as a percentage.
chamberId	Chamber ID	text			The laboratory identifier of the chamber used for this culture.

Illustrative payload:

{
    "humidityPercent": 1.0,
    "chamberId": "text"
}

Oxygenation log

• type code Oxygenation · version 1.0.2 · schema

Logs oxygenation of a bath or chamber, with the applied gas mixture and flow rate, measured dissolved oxygen or partial pressure, and the measurement method, location, device and calibration.

Property	Title	Shape	Required	Allowed values	Meaning
gasComposition	Gas composition	text			Applied gas mixture, for example 95% O₂ / 5% CO₂.
flowRate	Gas flow rate	quantity with unit		units mL/min, L/min; default {"unit": "L/min"}	The perfusion flow rate during this log event.
dissolvedOxygen	Dissolved oxygen or partial pressure	quantity with unit		units %, mg/L, mmHg; default {"unit": "%"}	The dissolved-oxygen concentration or oxygen partial pressure at the measurement location.
measurementMethod	Measurement method	choice		one of applied_gas_only, optical_sensor, electrochemical_sensor, blood_gas_analyser, other	The instrument or method used to obtain this measurement.
measurementLocation	Measurement location	text			The location within the chamber, bath, or specimen where the value was measured.
deviceIdentifier	Device identifier	text			The identifier of the device, chamber, or instrument used for the measurement.
calibrationReference	Calibration reference	text			Calibration date, certificate, or reference for the oxygen sensor.

Illustrative payload:

{
    "gasComposition": "text",
    "flowRate": {
        "value": 1,
        "unit": "L/min"
    }
}

pH log

• type code PH · version 1.0.2 · schema

Logs a pH measurement of a bath, chamber or sample, with measurement temperature, method, location, device and calibration.

Property	Title	Shape	Required	Allowed values	Meaning
ph	pH	number		≥ 0 and ≤ 14	Measured pH value.
measurementTemperature	Measurement temperature	quantity with unit		units °C, K; default {"unit": "°C"}	The temperature at which the pH measurement was made.
measurementMethod	Measurement method	choice		one of electrode, indicator_strip, calculated, other	The instrument or method used to obtain this measurement.
sampleLocation	Sample location	text			The bath, chamber, or sample location from which the pH value was obtained.
deviceIdentifier	Device identifier	text			The identifier of the device, chamber, or instrument used for the measurement.
calibrationReference	Calibration reference	text			Calibration date, buffers, certificate, or reference for the pH device.

Illustrative payload:

{
    "ph": 1.0,
    "measurementTemperature": {
        "value": 1,
        "unit": "°C"
    }
}

Temperature log

• type code Temperature · version 1.0.2 · schema

Logs a temperature measurement in a chamber, bath or specimen, with measurement location, method, device and calibration.

Property	Title	Shape	Required	Allowed values	Meaning
temperature	Temperature	quantity with unit		units °C, K, °F; default {"unit": "°C"}	Measured temperature at the stated location and time.
measurementLocation	Measurement location	choice		one of bath, incubator, chamber, specimen_surface, storage, room, other	The location within the chamber, bath, or specimen where the value was measured.
measurementMethod	Measurement method	choice		one of probe, thermocouple, infrared, incubator_sensor, other	The instrument or method used to obtain this measurement.
deviceIdentifier	Device identifier	text			Identifier of the calibrated measurement device when available.
calibrationReference	Calibration reference	text			Calibration date, certificate, or reference for the measurement device.

Illustrative payload:

{
    "temperature": {
        "value": 1,
        "unit": "°C"
    },
    "measurementLocation": "bath"
}

Health Logs

Slice health log

• type code SliceHealth · version 1.0.2 · schema

Logs an assessment of slice health, with overall rating, assessment method and scoring criteria, observed indicators, estimated viability, the context (e.g., before or after recording) and assessor blinding.

Property	Title	Shape	Required	Allowed values	Meaning
healthRating	Overall health rating	choice		one of excellent, good, fair, poor, non_viable, not_assessed	Overall assessment using the stated method and scoring scale.
assessmentMethod	Assessment method	choice		one of visual, electrophysiology, imaging, viability_assay, other	The observation or assay method used to assess slice health.
indicators	Observed indicators	multi-select		one of normal_appearance, torn, swollen, opaque, necrotic, contaminated, other	The observed features used to judge slice health.
viabilityPercent	Estimated viability (%)	number		≥ 0 and ≤ 100	The estimated viable proportion of the assessed cells or tissue as a percentage.
scoringScale	Scoring scale or criteria	text			The scoring scale or decision criteria used for the health assessment.
assessmentContext	Assessment context	text			For example recovery, pre-recording, post-recording, or culture day.
assessmentBlinding	Assessment blinding	choice		one of blinded, unblinded, unknown	Whether and how the assessor was blinded during the health assessment.

Illustrative payload:

{
    "healthRating": "excellent",
    "assessmentMethod": "visual"
}

Viability assay

• type code ViabilityAssay · version 1.0.2 · schema

Logs a viability assay on cells or tissue, with the assay type, percent viability and total cell count.

Property	Title	Shape	Required	Allowed values	Meaning
assayType	Assay type	text			The assay or measurement method used to estimate viability.
viabilityPercent	Viability (%)	number		≥ 0 and ≤ 100	The estimated viable proportion of the assessed cells or tissue as a percentage.
totalCellCount	Total cell count	integer		≥ 0	The total number of cells included in the viability calculation.
notes	Notes	text			A concise qualification of the viability assay result.

Illustrative payload:

{
    "assayType": "text",
    "viabilityPercent": 1.0
}

Observation Logs

Generic observation

• type code GenericObservation · version 1.0.0 · schema

Logs a free-form observation on a specimen set when no specific log type 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.