Thursday Morning - 3D TEM tomography/serial sectioning

  • studying flagellas
  • low SNR -> averaging multiple reconstructions of single particles
  • arrangement of dynein influences stroke pattern
  • bacterias from deep (106m) sea vents
  • neuron identification
  • 15x15x15um volume contains olfactory bulb
  • correlation of confocal microscopy stack with EM-Images
  • camera distortion gives same non-linear transformation in all images
  • different regions of same sample define camera distortion
  • Plugin to Fiji
  • Random forest classifier after training

Thurday Noon - Correlative Microscopy

  • fluorescence microscope coupled with x-ray "detection"
  • since imaging thick samples (pipette tip) is possible, no more missing wedge problem
  • Oxygen diffusion rate assessment on multiple oxides
  • 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

  • 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
  • Back-projection and re-projection to iteratively see 3D-reconstruction of sample
  • Neurontracking in 3D
  • SEM tomography -> analysis of filament network in cancer cells
  • skeletonization with Amira
  • Geostoch Software