Capturing a beautiful neuron

Today, I thought I’d share this beautiful 3-D reconstruction of two embracing neurons in the mouse brain, made by my labmate Julian Bartram. For those who are interested, I will briefly explain why images like this are useful (it’s not all about aesthetics!) and how they can be made in the lab.

Entorhinal cortex neuron


Researchers often record from the membranes of neurons to examine how they respond to various events such as exposure to particular drugs. As an example, it could be interesting to investigate how brain cells are influenced by substances such as picrotoxin, which is known to trigger epileptic seizures in animals, as studying this might offer some insights into how epilepsy affects the human brain. For this purpose, researchers might spend several weeks or months recording from the membranes of various neurons in brain slices taken from mice, while applying droplets of picrotoxin to the tissue.

After each recording, it can be immensely useful to verify the identity of the cell from which the information was collected. Is this a cell which releases the neurochemical dopamine? Or perhaps a neuron which sends signals using molecules of GABA – a chemical which inhibits other cells? Does this neuron have connections only with its immediate neighbours, or does it have long branches which project to a distant brain region, allowing the neuron to have a greater sphere of influence? Answering these questions can be important because the brain is chock full of neurons varying in size, shape, and structure, which makes each cell type quite distinct in terms of the functions it fulfils. The image below is just a snapshot of the astonishing diversity of brain cells we can find in the mammalian brain.

Cell diversity

Sometimes, when we insert an electrode into a brain slice to record from a neuron (shown below), we are essentially fishing, as it’s unclear what type of cell we are probing. PatchingIn fact, most often when we examine a brain slice through the microscope to aim for a neuron, they all look pretty much like blobs, as you can see in the image below, which I took last year in a lab where I previously worked.

MypatchThus, producing detailed images of the neurons from which we collect information can be important, since in times of uncertainty, they can help us identify cells by examining their structure. So how is this done?

Before diving into the brain slice with a micro-pipette to make a recording, the pipette is filled with a fluid which contains a particular protein – most often, biocytin. This means that once the micro-pipette reaches the chosen neuron and pricks its membrane to begin recording its activity, the liquid starts leaking into the cell, filling all of its branches within minutes. When the recording is completed, the brain slice is bathed in a liquid containing molecules of another protein which latch onto the biocytin proteins found inside the neuron. Importantly, each molecule of this protein comes with a so-called fluorophore – a chemical compound which can be forced to glow with a coloured light if it is excited by light of a different colour. What we now have is a neuron that is filled with a potentially fluorescent chemical – all we need to do is excite it and make snapshots of the light that it releases to begin making an image of the cell.

One type of microscope which is quite popular for doing this is the two-photon microscope, which works roughly like this:  twophotonAnd voilà – when you stack together the images produced by the fluorescence emitted from within the neuron across multiple depth planes, you end up with a detailed 3-D reconstruction like the one my labmate produced! Before we go on with our days, let’s just have a moment of appreciation for one of the most beautiful and complex types of neuron: the Purkinje cell of the cerebellum, a region in the back of our brain which is responsible, in part, for coordinating movements.



6 thoughts on “Capturing a beautiful neuron

  1. Hey! My labmate, Julian, used the ImageJ software (he also recommends the Fiji image processing package). Imaging the slice took roughly 5 minutes, and the 3-D rendering of the cell, once uploaded using ImageJ, was almost immediate.


  2. That was fast. I used ImageJ earlier but for reconstructing a single image it took me almost a week. Could you please connect me to yoru labmate. I have some things to learn from him 🙂


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