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Workshop: Helen Ramsden and David Willshaw, Chair: Jono Millin

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  • ANC Workshop Talk
When Oct 30, 2012
from 11:00 AM to 12:00 PM
Where If 4.31/4.33
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Helen Ramsden

Neurons in the mouse medial entorhinal cortex (MEC) encode an animal’s position in space, and are therefore of interest for understanding the cellular mechanisms of spatial coding. Behavioural and physiological data suggest that the network is functionally organised such that cells at different locations exhibit systematically different intrinsic properties, which may in part be genetically determined. To probe such differences, we have investigated the genome-wide genetic profile of the MEC using the Allen Brain Atlas (ABA) database of over 20000 images of in situ hybridisation (ISH) in tissue sections from more than 5000 mice. Extracting data from such images is limited in two major ways: (1) quality of tissue staining and (2) precise registration of the images across different animals and tissue sections. Although the ABA has addressed both problems, the accuracy of registration in the region of MEC is a clear area for improvement. By using a binary SVM classifier and two-dimensional non-linear registration, we have been able to (a) classify all database images based on the medio-lateral (z) location of the tissue segment, (b) improve their (x-y) alignment by registering them to a median image corresponding to their medio-lateral location, and (c) extract the expression information for a large proportion of genes, to the point that we can identify layer-specific expression and gradients within MEC. However, we currently have no explicit empirical test of the accuracy of registration, thus limiting our confidence in automated identification of enrichment beyond images that have been also been visually assessed.


David Willshaw

Local and global order in visuotopic maps

The topographically ordered projection of the retina onto the superior colliculus (or optic tectum) in vertebrates has been used as a paradigm system for investigating how ordered nerve connections are made. In the mouse it is possible to knock out the genes thought to control certain parts of the mechanism responsible for these connections and then examine what effect each knock out has on the connections formed. I've been analysing mapping data from the mouse visual system from both wild types and knock outs.

The analysis reveals that in the maps on the colliculus from animals where the molecules thought to specify order along one axis of the map have been removed by knockout of the appropriate genes there is still considerable order along this axis. I will show the evidence for this and then discuss the alternative hypotheses that are consistent with the data.