Articles

Fast Loop mesh subdivision in matlab

30th September, 2011

Progressive subdivision of a surface

Progressive subdivision of a surface

This matlab function sub-divides surface meshes, using the Loop subdivision algorithm. Because this algorithm is based on B-spline curve continuity, the surface is smoothed with only small distortions. The boundary of the surface is also left essentially undistorted.

Loading ImageJ ROIs into Matlab


No Java required!

10th August, 2011

There didn't appear to be an easy way to import ImageJ ROI files into Matlab, and the existing function I found didn't seem to work. This function imports ROIs and ROI sets without needing Java.

Rapid reading of TIFF stacks for Matlab, with lazy loading


memmapfile for TIFF files

24th July, 2011

A stack of two-photon data

A stack of two-photon data

Some two-photon imaging systems store data as three- (or more-) dimensional image stacks, stored in TIFF files. These are quite unwieldy if you need to process them in Matlab, since it is usually required that the entire stack is loaded into memory. Matlab does not offer an equivalent to memmapfile for TIFF files, so I wrote one myself.

Workshops at Capo Caccia 2011


Competition and cortex in Sardinia

29th April, 2011

View from the hotel

View from the hotel

This year at Capo Caccia we will be thinking about how competition in cortex can explain responses to natural stimuli, and wondering what the anatomy of competitive networks look like.

Daisy framework projects

24th January, 2011

A collaborative effort.

A collaborative effort.

A bulk injection of a neural tracer, made into the centre of the figure, reveals the tangential patterns of the axonal arbors made by neurons near the injection site. The neurons cooperate to form a complex and almost periodic pattern of projections across the cortical surface. Redrawn from Yoshioka et al. 1993.

When injections of dye are made into the upper layers of cortex, a remarkable structure of neuronal connectivity is revealed. Dye is absorbed by neurons and transported along axons and dendrites to fill entire cells. When a large population of neurons is stained in this way, slices examined in tangential section show a semi-regular array of denser staining.