Organoid Electrophysiology with IntraSense+: Questions and Answers

NeuroNexus · neuronexus.com · Resources

IntraSense+ records from inside intact brain organoids with penetrating silicon probes, in a sample chamber that runs inside a standard incubator, with a camera on the interface and Radiens ↗ for acquisition and analysis. It is configured for organoids of 2 to 5 mm, 16 to 256 channels, 1 to 8 shanks, and is available by quote. The questions below cover what researchers ask before a first recording.

Research use only. NeuroNexus products are for non-clinical research use and must not be used in human or veterinary medical procedures.

Can I record from inside a brain organoid rather than from its surface?#

Yes. IntraSense+ places silicon probe shanks into the organoid, so the electrode sites sit at chosen depths and lateral positions within the tissue rather than at the one surface the organoid rests on. The shank length and the site layout are chosen to meet the neuronal layers under study, and multiple shanks or entry points sample more than one internal location. The recording is extracellular: fast transients give spikes from nearby neurons, and the lower-frequency local field potential reports population activity, the spontaneous spiking and network oscillations that human cortical organoids are known to develop (Trujillo et al., 2019; Sharf et al., 2022). The method and example recordings are in IntraSense+: Electrophysiology Inside Intact Organoids.

How is that different from a planar multi-electrode array?#

A planar MEA records where the tissue meets the array, so it maps activity across the organoid's contact surface. A penetrating probe records from the interior, at depths and positions the experimenter selects, which is what a question about a particular cellular layer, a comparison across depths, or several entry points into one organoid requires. The two are different spatial views of the same tissue. In a NeuroNexus comparison on seven-month cortical organoids from one culture plate on one day, penetrating recording and a commercial planar CMOS MEA both detected spiking, with comparable spike detection; the difference was where the sites were, not whether they recorded.

What organoid sizes does it work with?#

The system is configured for organoids 2 to 5 mm in diameter. The sample chamber holds the organoid in a basket without compressing it and without attaching it to a planar substrate with an adhesion coating, and shank length (3 to 10 mm) and site placement are chosen so that the site-bearing segment ends up in the intended region of an organoid of that size. Smaller or larger preparations are a configuration question for a NeuroNexus Application Scientist.

Should I use a 2D or a 3D probe geometry?#

Both place sites inside the organoid; they differ in how the sites are arranged. A 2D probe puts its sites in one plane, at selected depths and lateral positions, and is the choice when the question is about a layer or a depth profile along one trajectory. A 3D array distributes sites across more than one plane and is the choice when the question compares internal regions or depths within one organoid at the same time. Probe geometry and site layout, linear, Buzsaki, polytrode, tetrode, edge or custom, are selected together against the organoid model and the endpoint.

How many channels can I record?#

16 or 32 channels with the integrated drive mount, and 64, 128 or 256 channels with an external drive. Probes have 1 to 8 shanks, 3 to 10 mm long, on 15 or 50 µm silicon. The channel count sets the connector and the headstage in the usual way, and the drive sets how the probe is positioned; the integrated mount covers the two smaller counts without extra hardware.

Can I stimulate as well as record?#

Yes. Sites are SIROF (sputtered iridium oxide film) or Z-Coat™, both with low impedance and high charge-storage capacity. Low impedance gives a low noise floor for recording; charge capacity lets a site deliver stimulation current within safe limits. The same probe can be configured to record and stimulate, with charge-injection limits and operating parameters set for the chosen stimulation protocol and a record-and-stimulate acquisition path specified at order.

Does it run inside my incubator?#

Yes. The recording assembly, with probe positioning, sample support and the camera, is built for use inside a conventional cell-culture incubator, so the organoid stays in its culture environment during the recording. Medium management, gas conditions and tissue-health measurements remain part of your own protocol. Cable management and a stable base let the assembly be moved between experiments, and a supplied cleaning system supports electrode reuse within your cleaning and inspection routine.

Can I watch the probe go in?#

Yes. The integrated camera gives a close view of the shanks as they enter the organoid while the traces are shown live in Allego, so insertion depth is adjusted on both the picture and the signal. Changes in activity across sites as the probe advances are the functional guide to the target layer. The organoid is retrieved intact after the probe is withdrawn.

Can I record the same organoid across days?#

Yes. Penetrating access and incubator-compatible operation support longitudinal studies: the organoid is recorded, returned to culture, and recorded again, with results that stay tied to the same sites and specimen. Rasters from one preparation on two days, with network bursts marked, are shown in the application note. Event timing, firing patterns and network features are compared across sessions of maturation, perturbation and recovery, with the culture record as the biological context for any change.

What does the software give me?#

Radiens connects acquisition, spatial display, analysis and curation. Allego ↗ acquires and shows the live signal with per-channel quality, signal-to-noise ratio, noise floor and activity, and a 3D view that places activity on the probe geometry with the organoid model in the same space. Videre ↗ runs spike sorting, field-potential and spectral analysis, and curation that keeps channel and window selections non-destructive with processing history retained. Local storage, NWB ↗ export and RadiensPy ↗ connect the data to your own analysis in Python.

Can I use my own acquisition system and software?#

Yes. NeuroNexus probes connect to compatible third-party acquisition systems through the usual headstage and adapter path, and Radiens reads files from other acquisition software and writes NWB, so a laboratory can add the probes and the organoid platform to the recording hardware and analysis it already runs, or adopt the whole system. Which parts to take is a configuration decision made with an Application Scientist.

How many sites actually record activity?#

In one NeuroNexus technical dataset, activity was detected at 834 of 1,056 electrode sites, about 79%. The dataset behind the application note holds about 130 recording sessions and 633 recordings, about 1 TB. The fraction is site-based and belongs to that dataset's organoid model, site placement and recording conditions; it is read with them, not as a specification. How signal quality is measured and reported during a session is covered in the application note, which is also available as a PDF ↗. To configure a system, start at Organoid Electrophysiology.