Homework 5.2: Caulobacter growth (50 pts)¶
Dataset download (about 600 MB)
In this problem, we will study the growth and division of Caulobacter crescentus over time. The lab of Norbert Scherer at the University of Chicago acquired these data and published the work in PNAS, which you can download here.
The clever experimental set-up allows imaging of single dividing cells in conditions that are identical through time. This is accomplished by taking advantage of a unique morphological feature of Caulobacter. The mother cell is adherent to the a surface through its stalk. Upon division, one of the daughter cells does not have a stalk and is mobile. The system is part of a microfluidic device that gives a constant flow. So, every time a mother cell divides, the un-stalked daughter cell gets washed away. In such a way, the dividing cells are never in a crowded environment and the buffer is always fresh. This also allows for easier segmentation.
The data are available here. They were kindly provided by Charlie Wright and Sri Iyer-Biswas in the Scherer lab. The frame rate is 1 frame per minute. The interpixel spacing is 0.052 µm. All images were acquired at 24 \(^\circ\)C.
As with any of the problems in this class, you are encouraged to explore the data beyond what is asked for specifically in the problems statements. The paper is also a very interesting read.
a) The directory sequential_full_field contains 10 sequential frames of a full field of bacteria in the microfluidic device. From these frames, choose which bacteria would be good to use to gather long time course imaging. I.e., choose those that you think will give minimal errors in segmentation. Give your reasoning, including images demonstrating segmentation.
b) The files bacterium_1.tif and bacterium_2.tif are TIFF stacks of time courses for specific cells in from the full field images. From these time courses, determine the bacterial area for each time point. For each bacterium plot the bacterial area versus time.
Looking forward: In the next homework, you will continue working with this data set. You will be asked to do the following:
Assign each time point with an identifier for which division event is. That is, the first few frames lead up to the first cell division, the first few frames after the first division event belong to the second, and so on. This means you need to determine when divisions happen.
Make an informative plot of the time between divisions for each cell and plot the results. Comment on any interesting aspects of these data.
If you feel like working ahead, you may do so. Whether you do or not, be sure you save your results in a CSV file for future use.