Master thesis defence by Hans Jacob Teglbjærg Stephensen

Supervisor: Jon Sporring
External Examiner: Rasmus Larsen, DTU

Biophysical Parameter Estimation Using Image Analysis — Distribution of organelles using shortest path metrics on the intracellular space of the neuron active zone

Measuring distances inside of animal cells is usually done without regard for obstructing structures or organelles, but as a straight line in euclidean space between two points of in- terest.

This does not accurately represent the distances inside of nervous system cells, as they bend through the tissue and contain a numerous amount of obstructing organelles. Using shortest path distance functions as an alternative, this thesis presents the needed methods for accomplishing this as well as an implementation in a complete software suite for image and data handling, segmentation and annotation of organelles, as well as distance function calculations.

The software was then subsequently used to annotate organelles present in the active zone of the visible part of 3 neurons in their entirety using a public FIB-SEM dataset. From this data, statistical analysis of the organelles and inner volume near the pre-synaptic area was performed.

By examining the results, I conclude that the methods described may likely be used in the future as an alternative perspective on the neuron. Using the data, I speculate that the bulging of the neuron near the active zone is due to the presence of or- ganelles. I propose ideas as to why the central compartment of the active zone area seem to be dominated by vesicles. I also conclude, that while a lot of cytosol is present in the annotated neurons, it doesn’t seem to be concentrated in any one place.