What is my research about?

Developing a set of open-source computational tools in Python to perform multi-scale analysis of structure-function relationship in mitochondrial networks. My model organism is Saccharomyces cerevisiae, also known as budding yeast.

Segmentation of mitochondrial networks from live yeast cells 3D images taken with a spinning disk confocal microscope

• The segmentation pipeline utilizes MitoGraph, a C++ skeletonization and segmentation program developed by Matheus Viana. It has been fully validated in yeast cells (Viana, Lim et al.).
• The pipeline folder contains modules used to map mitochondrial function to structure. This pipeline utilizes Mayavi’s version of VTK which contains convenient Python wrappers for VTK functions.
• This notebook shows an example of a typical workflow.
• The output data from the pipeline was ‘munged’ into a database using Pandas before further calculations of various statistical and functional parameters.

Modulation of mitochondrial function by altering carbon source growth conditions

• We modulated the metabolic state of the cell by altering the carbon source used during cell growth. This notebook shows an example of how carbon source growth conditions alters oxygen consumption and mitochondrial membrane potential (Δψ), which is a key parameter of cell bioenergetics.

Investigating the link between structure of mitochondria and heterogeneity of mitochondrial membrane potential (Δψ)

• We showed the non-random heterogeneous distribution of Δψ within a single mitochondrial tubule example here.

• We also detail our investigation into the relationship between heterogeneity of mitochondrial function and network topology example here.

Analysis of mitochondrial functional asymmetry in mother and daughter yeast cells

• A set of tools to interactively visualize the 3D mitochondrial skeleton and pick points to classify the cell as a mother or daughter region. This Ipython notebook demonstrates an application of these tools to study how mitochondrial membrane potential (Δψ) is distributed differently between the mother and daughter cell.

Requirements

If you wish to download the source code for the pipeline, you need to have these dependencies installed:

• Pandas
• Matplotlib
• Mayavi**
• NetworkX
• Numpy
• Seaborn
• Scipy
• VTK

**MayaVi has a known conflict when run under IPython and Python 2.7, specifically incompatible API versions. To fix, set QT_API=pyqt under your enviroment variables, either in BASH or Windows advanced settings. The best way to ensure all dependencies are fulfilled is by installing the Anaconda Python package.