Today, we all — biologists or not — have an idea about how the brain functions. The advanced techniques and lab procedures have made the knowledge accessible and unlocked many mysteries related to brain functioning.

One such procedure is brain slicing. It’s a process in which parts of the brain are divided using advanced technologies or microtomes in desired plane or orientation.

The process helps scientists to understand the underlying pathophysiological conditions of the brain, its development, and its responses to several stimuli. By using a brain slice in controlled physiological conditions, you can study a synapse or neural circuit in isolation from the rest of the brain.[1]

Furthermore, as the brain slice retains the brain’s 3D structural integrity, one can examine the electrophysiological consequences of drug toxicity.[2]

During the process, the brain is sliced using a tissue slicer. Then, to stimulate the particular brain area and record data, the slice is immersed in artificial cerebrospinal fluid (aCSF).[2]

This article is an exposé on brain slicing, including the directions and planes of slicing, equipment used in the procedure, and the applications of the technique.

Directions and Planes of Brain Slicing

Before moving to the directions and orientation of brain slice preparation, have a look at some directional terms. These directions also represent the possible views of different parts of the brain during studies.[3]

  • Lateral: Side view
  • Medial: Towards the midline (as in the sagittal section—see the next paragraph)
  • Dorsal: Top view or looking from the top
  • Ventral: Looking from down
  • Rostral: Towards the nose/beak. Here, the part above the midbrain is known as anterior and the one below the midbrain is called superior.[4]
  • Caudal: It means towards the tail. Here, the part above the midbrain is considered posterior, and below the midbrain is called inferior.[4]
A schematic diagram of different regions of the brain and their scientific terms

Figure: A schematic diagram of different regions of the brain and their scientific terms.[3]

Furthermore, a 3-dimensional brain has three planes, which also represent the ways a brain can be sectioned for experimental procedures:

  • Horizontal plane: A horizontal slice of the brain separates the top part of the brain from the bottom.[3]
  • Coronal plane: This divides the front section of the brain from the back section.
  • Sagittal plane: Here, the brain is divided into left and right parts. However, the midsagittal plane cuts the brain precisely in the middle, creating an equal division between the right and left hemispheres of the brain.[3]

Figure: An illustrative diagram of different planes of the brain.[5]

Equipment Used to Prepare Brain Slice

Brain slice preparation is a high-throughput procedure that requires expertise and knowledge of the equipment, tools, and chemicals to precisely perform the procedure based on experiential requirements.[6]

The Compresstome VF-200 slicing machine is the commonly used slicer in a range of life sciences labs to prepare brain slices including:[6]

The machine uses agarose embedding of the tissue and slight compression to make fine and uniform tissue slices.

Other than the Compresstome VF-200 slicing machine, you also need the following equipment and tools to perform the brain slice procedure:[6]

Slicing chamber

These are used to house or culture brain slices.[6] It’s of different types, which include:[7]

  • Interface slice chamber: The chamber anchors the brain slice between hyper oxygenated aCSF and air — usually humidified at 95% O2 or 5% CO2. The top surface of the brain slice is exposed to pO2 while the bottom rests on a nylon sheet for an exchange of nutrients or waste with aCSF from underneath. The limitation of the chamber is that it affects the optical and physiological properties of the brain slices over time.[7]
  • Submerged slice chamber: It’s also known as the superfusion chamber. It provides improved control over aCSF flow over the brain slice and faster exchange of toxins or drugs compared to the interface chamber.[7]
  • Organotypic slice chambers: In this technique, the brain slice is spread out and settled into thin cell layers. This allows the development of new neuronal structures with the degeneration of a few neuronal fibers. Additionally, the technique also enables one to maintain the viability of the brain slices for weeks and even months. However, the technique is a time-intensive slice preparation.[7]
An illustration of different types of brain slice chambers: (A1) Interface chamber; (A2) submerged slice chamber; (B1) Organotypic slice chambers with interface chamber; and (B2) Organotypic slice chambers in a rotary tube

Figure: An illustration of different types of brain slice chambers: (A1) Interface chamber; (A2) submerged slice chamber; (B1) Organotypic slice chambers with interface chamber; and (B2) Organotypic slice chambers in a rotary tube.[7]

Besides these conventional slice chambers, advanced microfluidic devices are also available that provide improved oxygen penetration efficiency and enhance brain slice viability and functions.[7]

An illustration of a microfluidic device: (A) integrated into the linear experimental set-up; and (B) combined with conventional slice chambers

Figure: An illustration of a microfluidic device: (A) integrated into the linear experimental set-up; and (B) combined with conventional slice chambers.[7]


A range of blades are available in the market based on the materials used to manufacture them, such as highly-durable stainless steel, carbon steel feather blades, and ceramic blades.

Dissection tools

It includes tools such as fine dissecting “supercut” scissors (for cutting through the skull), fine spatula, heavy-duty spatula, curved blunt forceps, scissors for decapitation, scalpel handle, and 10-number blades.

Transcardial perfusion tools

It includes a large dish filled with Sylgard for pinning anesthetized animals, a 30 mL syringe with 25 5/8 gauge needles, and dissecting pins.

Multi-scale incubation chamber

The incubation chamber includes Brain Slice Keeper-4 or any other similar machine. However, it must have a fine gas diffuser stone for infusion of carbogen into the aCSF, a submerged netting for the slices to rest on, and some gentle constant flow to circulate the solution through the slice.

Vapor pressure osmometer

It should be calibrated frequently when in use and the thermocouple should be kept clean.[6]


It should be accompanied by a thermoblock and the temperature should be set at 42°C with the mixing speed at 600 rpm – this maintains the molten state of 1.5% low agarose before usage.[6]

pH Meter

 It should always be calibrated before use.

Other than these, others include a carbonate supply machine, electrophysiology rig, blue laser for ChR2 photostimulation experiments, and laser scanning confocal microscope.[6]

Advantages and Limitations of Using Brain Slice Preparations

Brain slice preparation and usage have several advantages over other conventional techniques, which also increased the implementation of the technique in some experimental studies, such as investigating mammalian CNS activity.

However, some limitations also need to be considered before applying the brain slice preparation and procedure in your lab protocol.


  • Great experimental control.[1]
  • Only focuses on the region of the brain circuit that is of interest.
  • Easy perfusion of substrates through the incubation fluid to carefully control the physiological conditions.[1]
  • Precise manipulation of neurotransmitter activities for research studies by perfusing agonists and antagonists.[1]
  • Compared to other in vitro platforms or experiments, the brain slice replicates many aspects of the in vivo regulations and environment.[8]
  • Brain slices preserve the tissue architecture of the brain region being studied. It maintains the neuronal activities with intact functional local synaptic circuitry of their origin.[8]
  • The brain slice procedure does not require lengthy animal surgery, laborious monitoring of multiple physiological parameters, model neuropathology of brain injury, or strictly following in vivo manipulations.
  • Brain slices support research on establishing clear links between molecular changes and neuropathological outcomes.[8]
  • The technique is faster and cheaper than in vivo approaches.
  • The procedure does not require the use of anesthesia after the initial sacrifice.[1]
  • It avoids the extension of intracellular recording by eliminating the mechanical effects of heartbeat and respiration.[1]


  • The use of removed or isolated brain slices is limited by the absence of usual inputs and outputs of a whole brain.[1]
  • Slicing the brain can compromise brain tissues, affecting the morphology and physiological properties of the tissues.
  • Isolating the brain induces aging in the tissues at a faster rate during recording compared to studies on the intact brain.[1]
  • There is no blood flow in brain slices, so substrates and oxygen must enter the cells through diffusion from the medium, causing damage to the cells at the end.[9]
  • Brain slices have a limited lifespan, which limits the time for scientists to conduct their studies on the brain’s neuronal properties.[9]

Related Read: Preservation Techniques: Methods for Preserving Tissue Slices


A brain slice is a result of sectioning a particular part of the brain in a specific plane or orientation using a sharp blade. The prepared slice allows us to study underlying pathophysiological conditions, a particular area of the brain and its neural circuitry, and the development of brain tissues and neural networks.

However, there’s a need to develop and introduce affordable technologies that are not labor and time-intensive, and most importantly, do not alter the properties of the tissues to obtain accurate and reliable data.

Though microfluidic technology has the potential to improve brain and neuronal studies, it requires further research to determine its effective applications in that area.

Are you looking for a tissue slice chamber that works in both submerged and interface modes? Check out our acrylic biochemistry dual-channel system.


  1. Slice preparation. Retrieved from
  2. In Vitro Micro-Tissue and -Organ Models for Toxicity Testing. Retrieved from
  3. Slicing Terminology. Retrieved from
  4. Nadia Solomon. Brain orientation difficulties. Retrieved from
  5. Directions and Planes of Section. Retrieved from,of%20the%20brain%20into%20parts
  6. Ting, Jonathan & Daigle, Tanya & Chen, Qian & Feng, Guoping. (2014). Acute Brain Slice Methods for Adult and Aging Animals: Application of Targeted Patch Clamp Analysis and Optogenetics. Methods in molecular biology (Clifton, N.J.). 1183. 221-42. 10.1007/978-1-4939-1096-0_14.
  7. Huang, Yu & Williams, Justin & Johnson, Stephen. (2012). Brain slice on a chip: Opportunities and challenges of applying microfluidic technology to intact tissues. Lab on a chip. 12. 2103-17. 10.1039/c2lc21142d.
  8. Cho S, Wood A, Bowlby MR. Brain slices as models for neurodegenerative disease and screening platforms to identify novel therapeutics. Curr Neuropharmacol. 2007 Mar;5(1):19-33. DOI: 10.2174/157015907780077105. PMID: 18615151; PMCID: PMC2435340.
  9. Mary C. McKenna, Gerald A.Dienel, Ursula Sonnewald Helle, S. Waagepetersen, and Arne Schousboe. Energy Metabolism of the Brain. Basic Neurochemistry (Eighth Edition), 2012, Pages 200-231.