Lederberg_2017-12-09

Session Required Single selection

The session during which the behavior was run. The choices are limited to sessions in projects where you can make changes, and the session supplies this entry's permission context.

Subjects Required Multiple selections

Every subject that took part. The choices come from the session's own subjects, so add a subject to the session first if it is missing here. Select all participants rather than creating one Behavior per animal, unless they genuinely ran separately.

Setup Required Single selection

The physical rig the behavior ran on. Only setups you can change are offered. Its setup type is shown beside the field so you can check the rig suits the assay.

Behavioral assay Required Single selection

The lab method performed. Only assays you can change are offered. This is what carries the task definition — the Behavior itself stores no task parameters.

Order Number

Where this behavior appears among the session's entries. Use it when the sequence within the session matters; it does not imply a start time.

Notes Text · 500 characters

What was specific to this occurrence: deviations from the assay, technical problems, or notable outcomes. Anything that repeats every run belongs on the Behavioral assay instead.

The selected type controls the structured fields under Data. No type has required detail fields, so record what you know. Types fall into a few detail shapes: channel-based types ask for channels, samples, and sampling rate; frame-based types ask for resolution, frame count, and frame rate; light-based imaging types add excitation wavelength and laser power. The descriptions below follow the same groups and order as the Type dropdown.

Audio and Behavior Tracking

Audio recordings and video or tracking data that capture the subject's sounds and behavior.

• Audio: A recorded sound signal, such as vocalizations or an acoustic monitor. Use this for the audio signal itself; a sound used as a stimulus is a Manipulation. Structured fields: file name, format, compression, bit depth, codec, channels, samples, and sampling rate.
• Behavioral Tracking: Derived or processed tracking data: positions, markers, key points or poses produced by a tracking system such as an OptiTrack motion-capture rig or a pose-estimation pipeline. Use this when the stored stream is the processed points; the raw footage is Video tracking. Structured fields: file name, format, compression, frame count, resolution, and frame rate.
• Video Tracking: Raw video recorded to track a subject's movements or behavior. Use this when the video itself is the stored data; processed points or trajectories derived from it are Behavioral tracking. Structured fields: file name, format, compression, frame count, resolution, and frame rate.

Electrophysiology

Recordings of electrical activity, from scalp EEG and peripheral nerve signals to extracellular and intracellular recordings of neurons.

• Electroencephalography (EEG): Large-scale electrical activity recorded from electrodes on or beneath the skull rather than from within the tissue. Also use this type for ECoG surface arrays, or Extracellular Electrophysiology when a dense array is recorded on a probe system with electrode groups and channel tags. Structured fields: file name, format, data type, channels, samples, sampling rate, least significant bit, electrode groups, and channel tags.
• Electroneurogram (ENG): Electrical activity recorded from a peripheral nerve, typically through a nerve cuff or hook electrode. Structured fields: as for EEG.
• Extracellular Electrophysiology: Spiking and field activity recorded outside cells with a probe, tetrode, or wire electrode. This is the usual choice for silicon-probe and tetrode recordings. Structured fields: as for EEG, including electrode groups and channel tags for probe layout.
• Intracellular Electrophysiology: Membrane potential or current recorded from inside a single cell, as in whole-cell patch or sharp-electrode recordings. Structured fields: file name, format, data type, channels, samples, sampling rate, and least significant bit.

Optical Imaging

Fluorescence and optical recordings, from fiber photometry and miniscopes to confocal, light field and one-, two- and three-photon microscopy.

• Confocal Microscopy: Imaging that rejects out-of-focus light with a pinhole to produce optical sections. Structured fields: file name, format, compression, resolution, frame count, frame rate, laser power, and excitation wavelength.
• Fiber Photometry: Bulk fluorescence collected through an implanted optical fiber. It yields a population signal rather than an image, so it has no resolution fields. Structured fields: file name, format, compression, frame count, frame rate, laser power, and excitation wavelength.
• Light Field Microscopy: Imaging that captures the light field in one shot so a volume can be reconstructed without scanning. Choose it for volumetric single-shot acquisition rather than plane-by-plane imaging. Structured fields: as for Confocal Microscopy.
• Miniscope Microscopy: Imaging through a head-mounted miniature microscope in a freely moving subject, usually above a GRIN lens. Structured fields: file name, format, compression, frame count, resolution, frame rate, laser power, and imaging depth.
• Single-Photon Microscopy: Widefield or epifluorescence imaging using single-photon excitation. Use this for conventional widefield calcium imaging. Structured fields: as for Confocal Microscopy.
• Three-Photon Microscopy: Multiphoton imaging using three-photon excitation for greater depth and reduced background than two-photon imaging. Structured fields: as for Confocal Microscopy.
• Two-Photon Microscopy: Multiphoton imaging using two-photon excitation, the common choice for in-vivo cellular-resolution imaging. Structured fields: as for Confocal Microscopy.

Magnetic and Functional Imaging

Structural and functional magnetic resonance imaging and magnetoencephalography.

• Functional Magnetic Resonance Imaging (fMRI): MRI acquired as a time series to follow activity-related signal changes. Use plain MRI for structural scans. Structured fields: file name, format, compression, frame count, resolution, frame rate, laser power, and imaging depth.
• Magnetic Resonance Imaging (MRI): Structural or anatomical magnetic resonance imaging. Structured fields: file name, format, compression, frame count, resolution, frame rate, magnetic field strength, and imaging depth.
• Magnetoencephalography (MEG): Magnetic fields produced by neural activity, recorded outside the head. Structured fields: file name, format, compression, frame count, resolution, frame rate, laser power, and imaging depth.

Tomography and Ultrasound

Tomographic and ultrasound imaging, including CT, PET, SPECT, optical coherence tomography and functional ultrasound.

• Computed Tomography (CT): X-ray tomography, typically for skeletal or implant anatomy and implant verification. Structured fields: file name, format, compression, frame count, resolution, frame rate, laser power, and imaging depth.
• Functional Ultrasound Imaging (fUS): Ultrasound imaging of cerebral blood volume as an activity proxy. Structured fields: as for CT.
• Optical Coherence Tomography (OCT): Interferometric depth-resolved optical imaging of tissue microstructure. Structured fields: file name, format, compression, resolution, frame count, frame rate, center wavelength, and bandwidth.
• Positron Emission Tomography (PET): Imaging of an injected radiotracer's distribution, used for metabolic and receptor mapping. Structured fields: as for CT.
• Single-Photon Emission Computed Tomography (SPECT): Gamma-emitting radiotracer tomography. It is distinct from PET in tracer and detector, not in what the row records. Structured fields: as for CT.

General and Time-Series Data

Sampled signals that no more specific acquisition type covers, such as analog inputs and sensor streams.

• General time-series: Use this catch-all for a sampled signal that no specific method above describes, such as a temperature, force, or auxiliary sensor trace. Describe the signal and its source in Notes, because the type name alone will not tell another user what was recorded. Structured fields: file name, format, data type, channels, samples, sampling rate, least significant bit, electrode groups, and channel tags.

Type of data acquisition Required Choice

Select the acquisition method recorded by this row. The selection controls the structured fields shown under Data.

Session Required Single selection

Select the session during which the data were collected. The choices are limited to sessions in projects where you can make changes, and the session supplies this entry's project permission context. The session's subjects or specimen sets decide which interfaces are offered below.

Experimental interfaces Required Multiple selections

Select the target-facing interfaces the signal was acquired through. The choices are the interfaces installed on the session's subjects or specimen sets, limited to the interface types that fit the selected acquisition type. The order in which you select them is stored, so list them in the order that matches your channel or stream layout.

Equipment Multiple selections

Setup is an optional form-only filter for this field; it is not stored on the Data acquisition. Select the reusable instruments used to acquire the data. Only setups you can change and the Equipment they contain are offered.

Data Varies by type Structured details

Structured fields defined by the selected type, covering the file, format, and acquisition parameters. No detail field is required, but values recorded here are searchable and comparable, while the same information in Notes is not.

Order Number

Controls where this acquisition appears among the session's other entries. Use it when the order of streams is meaningful; it does not imply a start time.

Image File

Attach a representative preview, such as a field of view or an example trace. This is illustrative only: it is not the acquired dataset and does not replace a data-storage entry.

Notes Text · 500 characters

Record deviations, quality problems, or other relevant context that the structured fields do not capture.

The selected type controls the structured parameter fields shown in the form. No type has required detail fields. Most types share a common core — amplitude or concentration, duration, profile, repetitions, and whether the stimulus was closed loop — so the descriptions below concentrate on what distinguishes each one. The order follows the Type dropdown.

Electrical and Magnetic Stimulation

Stimulation with electric currents or magnetic fields, through implanted electrodes, transcranially or by an applied field.

• Deep brain stimulation (DBS): Electrical stimulation delivered through an implanted electrode to a defined deep target. Use this rather than Electrical stimulation when the defining feature is the chronic deep-target implant. Structured fields: amplitude, duration, profile, duty cycle, repetitions, injection polarity, and closed loop.
• Electrical stimulation: General electrical stimulation through an electrode, including intracortical and peripheral stimulation. This is the default electrical choice when no more specific type applies. Structured fields: as for DBS.
• Electromagnetic field stimulation: Exposure to an applied electromagnetic field rather than current delivered through a contacting electrode. Structured fields: as for DBS.
• Transcranial electrical stimulation: Current applied through scalp or skull electrodes without penetrating the tissue, covering direct, alternating, and random noise variants. Record which variant was used in the profile and notes. Structured fields: as for DBS.
• Transcranial magnetic stimulation (TMS): Non-contact induction of currents in tissue using a magnetic coil. Structured fields: as for DBS.

Optical, Thermal and Ultrasound Stimulation

Stimulation with light, temperature change or ultrasound, including optogenetic stimulation.

• Optogenetic stimulation: Light delivered to drive or suppress genetically targeted cells. Record the wavelength, since it is what distinguishes excitation from inhibition for most opsins. Structured fields: power, wavelength, profile, duration, duty cycle, repetitions, and closed loop.
• Thermal perturbation: Deliberate heating or cooling of tissue, such as focal cooling used to silence a region. Structured fields: amplitude, duration, profile, duty cycle, repetitions, and closed loop.
• Ultrasound stimulation: Focused ultrasound used to modulate activity, as distinct from ultrasound used to image, which is a Data acquisition. Structured fields: acoustic pressure, acoustic intensity, duration, duty cycle, profile, repetitions, injection polarity, and closed loop.

Chemical and Pharmacological Perturbations

Delivery of drugs or other agents by injection, inhalation, superfusion, microperfusion or other liquid application.

• Liquid perturbation: A change of the fluid around the preparation or exposed tissue whose effect comes from the solution itself, such as an osmotic challenge, ionic substitution or a bath-medium switch. Local delivery through a probe is Microperfusion; a drug in the bath is Pharmacological superfusion. Structured fields: concentration, volume, profile, repetitions, flow rate, and closed loop.
• Microperfusion: Local delivery or exchange of a solution inside tissue through an implanted probe or line at low flow, as in open-flow microperfusion or reverse microdialysis. Use it when the agent reaches a small target volume; bath-wide changes are Liquid perturbation or Pharmacological superfusion. Structured fields: as for Liquid perturbation.
• Pharmacological inhalation: An agent delivered through the respiratory route during the session. Structured fields: concentration, flow rate, profile, volume, repetitions, and closed loop.
• Pharmacological injection: An agent injected during the session to perturb the system under study. A drug given as clinical care, such as analgesia or anesthesia, is a Procedure instead. Structured fields: as for Liquid perturbation.
• Pharmacological superfusion: An agent applied by bathing the preparation in solution, the usual route for slice and other ex-vivo work. Structured fields: as for Liquid perturbation.

Sensory Stimulation

Presentation of auditory, visual, tactile, odor or combined sensory stimuli to the subject.

• Auditory stimulation: A presented sound, such as a tone, click, or noise burst. Recording sound is a Data acquisition, not a Manipulation. Structured fields: amplitude, duration, frequency, modulation frequency, profile, duty cycle, repetitions, and closed loop.
• Multisensory stimulation: Two or more modalities presented as one designed stimulus. Use this when the timing between modalities is part of the experiment; record separate entries when the stimuli are independent. Structured fields: modalities, temporal relationship, duration, repetitions, and closed loop.
• Odor stimulation: A presented olfactory stimulus, usually delivered by an olfactometer. Structured fields: concentration, flow rate, repetitions, and inhalation phase.
• Tactile stimulation: A mechanical stimulus applied to the body surface, such as whisker deflection or a von Frey filament. Structured fields: contact type, stimulation site, force, duration, profile, repetitions, and closed loop.
• Visual stimulation: A presented visual stimulus, such as a grating, flash, or natural scene. Structured fields: stimulus types, stimulus position, duration, repetitions, and closed loop.

Type of manipulation Required Choice

Select the stimulus or perturbation recorded by this row. The selection controls the structured parameter fields shown below.

Session Required Single selection

Select the session during which the manipulation was delivered. The choices are limited to sessions in projects where you can make changes, and the session supplies this entry's project permission context.

Experimental interfaces Required Multiple selections

Select the interfaces through which the stimulus was delivered, such as an optic fiber, cannula, or stimulating electrode. The order in which you select them is stored, so list them in the order that matches your delivery configuration.

Equipment Multiple selections

Setup is an optional form-only filter for this field; it is not stored on the Manipulation. Select the reusable instruments that generated or controlled the stimulus, such as a laser, stimulator, or olfactometer. Only setups you can change and the Equipment they contain are offered.

Data Varies by type Structured details

Structured parameters defined by the selected type. No detail field is required, but repeatable parameters recorded here are searchable and comparable, while the same values in Notes are not. Numeric parameters carry their own unit, so record the unit you measured in rather than converting.

Order Number

Controls where this manipulation appears among the session's other entries. Use it when the sequence of stimuli is meaningful; it does not imply a start time.

Notes Text · 500 characters

Record exceptional context, deviations, or delivery problems. Parameters that repeat across sessions belong in the structured fields instead.

Name Required Text

What this segment is called, such as "Baseline", "Stimulation period", or "Recovery". Name it for what was happening, since the times alone will not tell a reader that.

Session Required Single selection

The session this segment belongs to. It supplies the epoch's permission context, and it also determines which behaviors, acquisitions, and manipulations can be linked below.

Start Duration

When the segment begins, in seconds from the start of the session. Leave it empty if the segment runs from the session's beginning.

End Duration

When the segment ends, in seconds from the start of the session. Leave it empty if the segment runs to the end of the session.

Behavior Single selection

The behavior running during this segment. The choices come from this session, and the same behavior may be linked to several epochs.

Data acquisitions Multiple selection

The streams recorded during this segment; concurrent recordings (video and electrophysiology, say) all sit on the one epoch. A data acquisition can belong to only one epoch per session — the pairing is enforced — so one already linked elsewhere is shown greyed in the palette, and dropping it here moves it.

Manipulations Multiple selection

The stimuli delivered during this segment. The choices come from this session, and the same manipulation may be linked to several epochs.