Ilaria Iuliani

Ilaria.iuliani@unil.ch

​

Course: Solving Biological Problems that require Math

DBC Group of Prof. Bergmann

March 3, 2023

​

Bacterial growth and division

at the single cell level

How do we study bacterial growth?

SINGLE CELL LEVEL EXPERIMENTS

Agar Pad

Microfluidic device Chamber

vs

The study of bacterial growth at single cell level is leading important discoveries in different fields (e.g. antibiotic tolerance/ persistence)

~ 1 frame/min

RAW DATA

IMAGE ANALYSIS

DATA ANALYSIS

The project

Aim:

Characterize E. coli growth and division at the single cell level by comparing different “size variables” (Length, Area, Volume, Width … )

( From published articles )

( From open-source tools)

( van Vliet et al. Cell Syst. 2018 )

Image analysis

( O’Connor OM et al. PLOS )

​

Many open-source and user-friendly tools exist:

​

DeLta (Deep Learning for Time-lapse Analysis)

SuperSegger

Omnipose

Cellpose

​

( Do we get similar results by using different tools? )

​

​

Two main steps:

​

SEGMENTATION:

generates information about cell morphology

​

​

TRACKING:

tracks cells across frames and records division events

​

​

​

( Romano et al. Phys. Rev. 2020 )

​

• Is cell length a good proxy for cell size?
• Is cell width also important? (or always constant?)
• How can we model E.coli shape?

e.g. cell volume can be computed considering a cell as a cylinder with two hemispherical caps

​

​

Estimation of different cell size variables

Data analysis

With these data,

​

• we can look at variables over time

(do they increase exponentially? How fast? …)

​

• we can look at variables at a given time (birth and division)

(are they correlated? Do they double from birth to division?...)

​

• we can look at correlations between mother and daughter or between sisters

Cell Size

Time

From image analysis

...

Main questions

Do different image-analysis tools give us the same information about E.coli cell size?

Which features can I easily get from images (Length, Area, Volume, Width…)?

QUESTION 1

How are these different “size variables” correlated at birth and division?

Do they all double from birth to division?

Are they strongly correlated between mother and daughters or sisters?

QUESTION 2

Do all these different “size variables” increase exponentially?

Can we define a new variable that tells me how fast they grow (growth rate)?

Do all cells have the same growth rate?

QUESTION 3

What you will learn

• Extract quantitative information from images

​

• Improve your R/Phyton skills for data handling and statistical analysis

​

• Correlation analysis

​

• Time series analysis

​

Ilaria Iuliani

Ilaria.iuliani@unil.ch

​

Bacterial growth and division

at the single cell level