What is a behavior core?

A behavior core is a shared facility or lab group that runs standardized behavioral assays for multiple projects. The core owns scheduling, apparatus readiness, animal acclimation, scoring quality, and documentation.

How do I design a mouse behavior battery?

Start with the least stressful assays, group tests by primary endpoint, protect recovery time after aversive tasks, and avoid placing one-trial anxiety assays after severe stressors.

How long should acclimation be before behavior testing?

Plan at least 7 days of room habituation before testing. Add structured handling for the 5 days before the battery, and use 14 days when reversing the light cycle.

What is a confounded test order?

A confounded order is a sequence where an earlier assay changes later behavior. Examples include forced swim before elevated plus maze, repeated one-shot anxiety tests, or a high stress load across one week.

What kappa is acceptable for behavior scoring?

Many labs target at least substantial agreement for categorical scoring, often kappa above 0.60, before unblinding study groups. The acceptable threshold should be predefined in the SOP.

How do labs validate scoring across raters?

Use a blinded calibration set, compare categorical states with Cohen kappa, compare continuous measures with ICC, resolve rubric ambiguities, then repeat calibration before the main cohort.

How do I write a behavior SOP?

A behavior SOP should define purpose, apparatus, animals, lighting, cleaning, procedure, exclusion criteria, scoring rubric, statistical plan, and references. It should be specific enough for another operator to reproduce the assay.

Run a Behavior Core

Plan, acclimate, score, document, and run rodent behavior batteries with five free browser tools.

Battery SequencerAcclimation TrackerIRR CalculatorEthogram BuilderSOP Generator

1. Plan your battery

Pick tests, then lint for confounded orders, one-shot repeats, stress overload, and recovery-window mismatch.

Study window (days)

1. Open Field

Recovery after: 1 day | one-shot: no

2. Rotarod

Recovery after: 1 day | one-shot: no

3. Elevated Plus Maze

Recovery after: 1 day | one-shot: yes

4. Forced Swim Test

Recovery after: 7 days | one-shot: yes

Confound report

No major sequencing warnings detected.

Estimated calendar

Day	Test	Paradigm	Stress	Links
1	Open Field	anxiety	1	Calculator/Apparatus
2	Rotarod	motor	2	Calculator/Apparatus
3	Elevated Plus Maze	anxiety	2	Calculator/Apparatus
4	Forced Swim Test	depression	5	Calculator/Apparatus

2. Acclimate animals

Cohorts

Battery start dateInclude 14 day light-cycle reversal

Day	Date	Activity	Cohort	Details
-7	2026-04-24	Room habituation begins	All cohorts	Move animals into the test suite or holding room at least 7 days before testing.
-6	2026-04-25	Room habituation	All cohorts	Keep husbandry, transport, noise, and room entry windows consistent.
-5	2026-04-26	Handling sessions	Cohort A	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-5	2026-04-26	Handling sessions	Cohort B	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-5	2026-04-26	Room habituation	All cohorts	Keep husbandry, transport, noise, and room entry windows consistent.
-4	2026-04-27	Handling sessions	Cohort A	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-4	2026-04-27	Handling sessions	Cohort B	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-4	2026-04-27	Room habituation	All cohorts	Keep husbandry, transport, noise, and room entry windows consistent.
-3	2026-04-28	Handling sessions	Cohort A	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-3	2026-04-28	Handling sessions	Cohort B	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-3	2026-04-28	Room habituation	All cohorts	Keep husbandry, transport, noise, and room entry windows consistent.
-2	2026-04-29	Handling sessions	Cohort A	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-2	2026-04-29	Handling sessions	Cohort B	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-2	2026-04-29	Room habituation	All cohorts	Keep husbandry, transport, noise, and room entry windows consistent.
-1	2026-04-30	Handling sessions	Cohort A	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-1	2026-04-30	Handling sessions	Cohort B	Three 1 minute handling sessions per animal, separated by at least 30 minutes.
-1	2026-04-30	Room habituation	All cohorts	Keep husbandry, transport, noise, and room entry windows consistent.
0	2026-05-01	Begin behavior battery	Cohort A	Run Cohort A at the same circadian phase and document transport order.
1	2026-05-02	Begin behavior battery	Cohort B	Run Cohort B at the same circadian phase and document transport order.

3. Score reliably

Walking

Locomotion with four paws, head forward.

Supported rear

Rearing with forepaws on a wall or object.

Body grooming

Licking or scratching trunk, flank, tail, or hindlimbs.

Sniffing conspecific

Nose-to-nose, nose-to-body, or nose-to-anogenital contact.

Freezing

Complete immobility except respiration for at least 1 second.

Add custom state

Two rater columns

Cohen's kappa

0.545

Moderate agreement

Interpretation follows Landis and Koch categories.

4. Document everything

TestSpeciesApparatusLightingCleaningExclusion criteria, one per lineScoring rubricStatistical plan

SOP preview

Purpose

This SOP defines standardized execution, scoring, and documentation for the Open Field in mouses.

Apparatus

Use Open Field Arena. Confirm apparatus dimensions, camera coverage, software project settings, and calibration records before the first animal is tested.

Animals

Test mouses after the approved acclimation and handling period. Maintain consistent transport order, holding conditions, and circadian timing across cohorts.

Lighting

Record lux at the arena floor before each testing block.

Cleaning

Clean with 70% ethanol between animals and allow surfaces to dry.

Procedure

Run Open Field according to the approved protocol. Record animal ID, group, cohort, start time, apparatus ID, software version, operator, and any deviations.

Exclusion criteria

- Tracking failure that prevents primary endpoint scoring - Animal escape from apparatus - Protocol deviation documented before unblinding

Scoring rubric

Score primary endpoints from blinded video files. Record start time, endpoint values, and tracking quality.

Statistical plan

Compare predefined groups using the approved model. Report n, exclusions, effect size, and confidence interval.

References

Crawley 2007; McIlwain et al. 2001; Bailoo et al. 2014; local IACUC protocol and lab SOP index.

5. Run the tests

Every test in the catalog links to its dedicated calculator at /tools/<test-name> and apparatus at /lab/<apparatus>. For automated tracking, see ConductVision.

Plan a multi-assay rodent behavior battery before reserving rooms or equipment
Build a day-by-day acclimation and handling schedule for cohorts
Check categorical scoring with Cohen kappa and continuous scoring with ICC
Assemble a project ethogram from curated rodent behavior states
Generate a draft SOP for apparatus, lighting, cleaning, scoring, and exclusions

Don't use for

Final veterinary or IACUC approval without local protocol review
Automated video tracking from raw video files
Persistent scheduling for a facility calendar

Resources

Battery order reviewed for stress and carryover
Room habituation and handling schedule assigned
Cleaning agent and dry time documented
Ethogram states operationally defined
Rater calibration completed before unblinding
Exclusion criteria written before scoring

Why Test Order Matters

A behavior battery is not just a list of assays. Each test can change arousal, fatigue, learning, pain sensitivity, social motivation, or anxiety-like behavior. Low-stress exploration and baseline motor checks usually belong early. Aversive or one-trial tests need careful placement because they can create carryover effects that are larger than the biology being measured.

Use the sequencer as a planning pass before calendar lock. The warnings do not replace protocol review, but they make common order effects visible while the schedule is still easy to change.

Acclimation That Actually Works

Acclimation is an experimental variable. Room transfer, reversed light cycles, handling, cage change timing, and transport order can all create cohort effects. A useful schedule names the day, cohort, activity, and handling dose so technicians can run the same preparation every time.

The tracker starts from the battery date and works backward. That keeps the first test from becoming the only fixed point while animal preparation drifts.

Reliable Behavior Scoring

Behavior scoring becomes reliable when raters share operational definitions. Ethograms convert vague labels into observable states, and IRR checks reveal where raters disagree before the main dataset is scored.

For categorical states, Cohen kappa is a compact check on agreement beyond chance. For continuous measurements, ICC(2,1) estimates absolute agreement between raters on the same subjects.

Frequently Asked Questions

About This Tool

Method: The sequencer uses typed assay metadata for stress, recovery, one-shot status, and caution pairs. The acclimation tracker generates deterministic rows from the battery start date. IRR uses Cohen kappa for categorical ratings and ICC(2,1) absolute agreement for continuous ratings. All computation runs in the browser.
Last Validated: 2026-04-30
Privacy: 100% client-side

Related Tools

How to Cite

ConductScience Behavior Core Workflow Hub (v1.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/behavior-core

Crawley JN. What's Wrong With My Mouse? Behavioral Phenotyping of Transgenic and Knockout Mice. Wiley-Liss. 2007.

McIlwain KL et al. The use of behavioral test batteries: effects of training history. Physiology & Behavior. 2001. doi:10.1016/S0031-9384(01)00528-5

Bailoo JD et al. Refinement of experimental design and conduct in laboratory animal research. ILAR Journal. 2014. doi:10.1093/ilar/ilu037

This hub supports planning and documentation. Local protocol approval, veterinary review, and statistical design remain the responsibility of the study team.

Why This Tool?

This hub keeps the behavior-core workflow in one stateless page: plan the battery, schedule animal preparation, validate scoring, define the ethogram, and draft the SOP.