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Registration of TEM images with TrakEM and bUnwarpJ


I work on reconstructing the first optic lobe in Drosophila, lamina, using TEM images of Drosophila brain serial sections.
In order to register my image stacks I use the ImageJ plugin bUnwarpJ in a serial mode to obtain a global registration, needed for the reconstruction.
I, also, use TrakEM to create registered montages of images. I create and align the montages at the same time.
A major problem is the folds in the serial sections, resulting in black lines crossing my TEM images. Hence, a simple affine transformation is not sufficient to register my images. However, the problem can be solved by automatic detection of landmarks and then applying the bUnwarpJ elastic registration.

Segmentation, registration, 3D viewer, reconstruction, Drosophila, neuroscience.

Marta Rivera-Alba and Gonzalo G. de Polavieja

Universidad Autonoma de Madrid


Short Biography   
I have BA in Theoretical Physics and a Master in Biophysics, both of them by the Universidad Autonoma de Madrid. Currently I am doing my PhD in the anatomy of Drosophila first optic neuropil, lamina, under the supervision of G. G. de Polavieja in the Universidad Autonoma de Madrid. I am specially interested in checking the optimization theories of brain anatomy in Drosophila, and in the predictions that I can obtain from that.

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