<markdown> # Thursday Morning - 3D TEM tomography/serial sectioning ## J.M. Plitzko - Cryo EM Tomography

## Khanh Huy Bui - Molecular architecture - studying flagellas - low SNR → averaging multiple reconstructions of single particles - arrangement of dynein influences stroke pattern

## R.Rachel - Serial Sections, back to 3D - bacterias from deep (106m) sea vents

## Christel Genout - Neuronal circuits in zebrafish - neuron identification - 15x15x15um volume contains olfactory bulb - correlation of confocal microscopy stack with EM-Images

## Verena Kaynig - Fully Automatic Distortion Correction of TEM Images - camera distortion gives *same* non-linear transformation in all images - different regions of same sample define camera distortion - Plugin to [Fiji](http://pacific.mpi-cbg.de/wiki/index.php/Main_Page) - [Random forest classifier](http://en.wikipedia.org/wiki/Random_forest) after training

# Thurday Noon - Correlative Microscopy ## Christopher Booth - Correlative Imaging of unstained cells - fluorescence microscope coupled with x-ray “detection” - since imaging thick samples (pipette tip) is possible, no more missing wedge problem

## S. Portier - Comparative study to examine oxides - Oxygen diffusion rate assessment on multiple oxides

## Stephan Gerstl - Analyzing Planar Microstructures via Atom Probe Tomography - Atom Probe Tomography, *extremely* high resolution analysis in 3D → detection of atoms in sample - coupled with mass spectrometer, so (ion mass, x, y, z) are output of measurement → detection of mass in volume

# Thursday Afternoon - 3D Image Analysis and simulation ## Robert F. Murphy - Location Proteomics → where are proteins located in cells - automated image analysis - co-occurrence matrix to detect “features” in 2D - tissue classification with computer can be even more accurate than human recognition - pattern detection for protein “family” - SCML (?) Toolbox - [openmicroscopy.org](http://openmicroscopy.org/)

## Jeremy David Woodward - 3D Reconstruction from Scanning Electron Micrographs - Back-projection and re-projection to iteratively see 3D-reconstruction of sample

## P. Levitz - Analysis of the topological evolution of an evolving pore network using 3D tomography - topological retraction at constant [betty number](http://en.wikipedia.org/wiki/Betti_number)s

## Eduardo Rosa-Molinar - Markers for Correlative Fluorescence - Neurontracking in 3D

## Aaron Ponti - Large-scale microscopy image processing and analysis - [Huygens](http://huygens-rm.org/) - [XuvTools](http://xuvtools.org/) - [Qu for MATLAB](http://qum.sourceforge.net/) - [HDF5](http://www.hdfgroup.org/HDF5/whatishdf5.html) files - tools for researcher - silly to present images on screen greater than 1024×768, rescale

## Sebastian Lück - Quantitative analysis of filament network - SEM tomography → analysis of filament network in cancer cells - skeletonization with Amira - [Geostoch](http://www.uni-ulm.de/mawi/mawi-stochastik/software.html) Software </markdown>