Tutorial Custom Analysis - veeninglab/BactMAP GitHub Wiki

Time-Lapse Analysis part 2: Custom analysis

Background

This tutorial is a follow-up of the tutorial on Temporal Localization.

In the 20s-interval movies of DnaX and FtsZ we analyzed for our preprint and in the tutorial on temporal localization, we observed that DnaX (the clamp loader of the DNA replication machinery) and FtsZ colocalize during much of the cell cyle, but FtsZ is appearing at the new septa at the quarter-positions of the cell earlier than DnaX. After the start of Z-ring formation, DnaX dissociates from mid-cell and replication is initiated at the new septa.

However, this observation is primarily based on the 7 cells out of the 20s movie I thought were suitable enough for analysis - to make a global comment like this, we need to look at more single cells undergoing a full division. For this reason, I re-analyzed a movie with longer time intervals. This would make the resolution lower, but the chance of catching more full divisions higher, since there is less phototoxicity.

Using this dataset, I will attempt to classify the cells based on the temporal DnaX localization.

Goal

This tutorial is meant as a taste of what you can do after using BactMAP. What you will learn about BactMAP on the way:

How to explore larger datasets with BactMAP
Doing crude classification of growth speed from time-lapse movies
Making kymographs based on moment in the cell cycle

Note

This tutorial is, even more than the previous one, a mix between BactMAP functions and other functions in R. It is meant as an example of how you could do analysis using R after using standard BactMAP functions for plotting. Instead of doing the whole tutorial on your computer (which is possible), you can also decide to just read through it and use the parts which are useful for you.