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Moved from a psychology degree to a PhD in neuroscience - an electrophysiological investigation of the sources of sensory input to dopamine releasing neurons. From there I moved back to psychology with an experimental postdoc looking at perception with sensory substitution devices. I am looking to move back into neuroscience with my next postdoc, but in the meantime I'm blogging on a mixture of psychology and neuroscience.

Automatic and reliable plotting of histology/recording sites

I feel a little bit guilty for coming back to use the blog for my own gain when I’ve not posted anything for a while, but I needed someone more permenant than twitter to ask for advice.

I’m trying to create a way of reliably plotting anatomical data like recording sites onto diagrams of brain structures, rather than exporting pages of a pdf atlas as images then copying and pasting symbols in Illustrator and moving them around until they look like they’re in the right place.

What I had in mind was some bit of code that would take stereotaxic coordinates of points (e.g. recording sites) and an image from a brain atlas and combine the two. The end result will be a bit like this.

I’m learning Matlab at the moment, so I’d planned to stick with that, but it doesn’t seem to deal with importing vector images very easily. My options now seem to be:

  1. try to plot the recording sites in Matlab at the appropriate scale without the images from the atlas, export the recording sites as a vector image, then combine the two in illustrator
  2. move back to R, which seems to handle vectors more readily (pdf guide)

Does anyone have any suggestions? Advice?



Trigeminal anatomy (in which my basic Adobe Illustrator skills improve)

I’ve been having a bit more of a practice with Adobe Illustrator (CS2), and with the help of these few posts from Prof Like Substance and a more extensive guide on the MIT website, and I can now do the basics without wearing out Ctrl, Z, and my patience. So here’s the fruits of the last hour or so’s efforts (click to embiggen):

The outlines of the trigeminal nerve ganglion and brainstem trigeminal nuclei in a rat (transverse section).

A diagram of the afferent and efferent connections of the brainstem trigeminal nuclei.

1: Lemniscal pathway

2: Paraemniscal pathway

3: Extralemniscal pathway

Abbreviations: 5G: trigeminal nerve ganglion; Pr5: principal trigeminal nucleus; Sp5o: spinal trigeminal nucleus oralis; Sp5ir: spinal trigeminal nucleus interpolaris, rostral subdivision; Sp5ic: spinal trigeminal nucleus, caudal subdivision; Sp5c: spinal trigeminal nucleus caudalis; SC: superior colliculus; Pom: medial part of the posterior thalamic nuclei group; VPM: ventral posterior medial thalamic nucleus; VPMvl: venterolateral region of the ventral posterior medial thalamic nucleus.

Science is beautiful, neurons are graceful, data are impressive

I like science. I also like things that look nice. That means I’m a sucker for things like the Brainbow transgenic mouse, where genes for a range of different fluorescent proteins are introduced into the mouse, producing pictures beautifully multicoloured slices of brain, like the one shown below.

A multicoloured slice of hippocampus from a Brainbow mouse.

Hippocampus: Broad Overview Tamily Weissman, Jeff Lichtman, and Joshua Sanes, 2005 from Portraits of the Mind: Visualizing the Brain from Antiquity to the 21st Century by Carl Schoonover

I’m drawn to anything with neurons on it, ties, shoes, t-shirts… My desktop background is an artists impression of dopaminergic neuron dendrites (I’m not sure how they look different from other neurons). It’s not just modern neuroscience that produces wonderful images though. The anatomist Santiago Ramon y Cajal produced stunning pictures of neuroanatomy that had been revealed by the Golgi staining method.

An illustration of the neuroanatomy of the olfactory bulb, by Camillo Golgi

Olfactory Bulb Camillo Golgi, 1875 from Portraits of the Mind: Visualizing the Brain from Antiquity to the 21st Century by Carl Schoonover

Cajal’s illustrations are immediately recognisable. People have painted them on canvas and tattooed them on themselves.

A comparison of Cajal's illustration of a pyramidal cortical neuron, and the same neuron revealed by Golgi staining

(I)Pyramidal neuron from postcentral gyrus, 1899 Santiago Ramon y Cajal (II) Photomicrograph of a Golgi preparation of postcentral gyrus, from the collection of Santiago Ramon y Cajal Museo Cajal from DeFelipe and Jones, Cajal on the Cerebral Cortex, 1988 source: Santiago Ramon y Cajal by Javier DeFelipe, MIT Encyclopedia of the Cognitive Sciences, MIT Press, Cambridge, MA 1998

I like to see data too. When I’m reading a paper I look for figures to help me interpret the results. When I’m designing my figures I want them to be attractive, but also clear and easy to understand. I’m a disciple of Tufte and a believer in the idea that information can be beautiful, but I also realise it can go very wrong.

Science shouldn’t look dull and boring. Science isn’t dull and boring, it’s full of a million and one unanswered questions and fantastical things you never knew. But in a busy world you might never know about them unless something catches your eye. Make your science catch someones eye, and when it does, have it tell the story of how you got there.

Hat tip and apologies to Bioephemera, whose two posts I stole the pictures from. And if a mystery benefactor would like to treat me to Carl Schoonover’s Portraits of the Mind: Visualizing the Brain from Antiquity to the 21st Century or David McCandless’s Information is Beautiful I would be a very happy man.

EDIT: The BBC have an impressive slideshow of the winners of the Wellcome Image Awards.

The brain as a network – a new hypothesis?

ResearchBlogging.orgThe BBC News Sci/tech section recently ran a few stories about neuroscience and technology that I considered to be a bit oversold. There was one article in particular I wanted to write about: Brain works more like internet than ‘top down’ company. The article refers to a recent study in PNAS that used injections of dye to trace connections between brain areas. The article claimed that it demonstrated that the brain is an interconnected network like the internet, counter to the apparently prevailing view of the brain as a hierarchy. The technique could also apparently lead to a map of the brain. Now, I was initially going to take the BBC to task for what seemed to be another oversold and rather general piece of research. However, after having a read through the paper, it seems that the authors may, to some extent, have oversold the novelty of the implications of the work, and the groundbreaking-ness of their technique. The line of reporting by the BBC only compounded the problem.

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