Data for: Tools and methods for high-throughput single-cell imaging with the mother machine

Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely-used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison..., The dataset consists of time-lapse images of E. coli cells grown in the microfluidic mother machine device. Images were obtained on an inverted microscope (Nikon Ti-E) with Perfect Focus 3 (PFS3), 100x oil immersion objective (PH3, numerical aperture = 1.45), and Obis laser 488LX(Coherent Inc., CA) as a fluorescence light source, and an Andor NEO sCMOS (Andor Technology) camera. The laser power was 18 mW. The exposure time was 200 ms for phase contrast imaging and 50 ms for fluorescence., , # Data for: Tools and methods for high-throughput single-cell imaging with the mother machine

### Overview

This dataset consists of unprocessed time-lapse imaging data of *E. coli* cells grown in the \"mother machine\" microfluidic device.

### Imaging conditions

`Imaging interval` 150 seconds

`Resolution` 0.065 uM / pixel

Images were obtained on an inverted microscope (Nikon Ti-E) with Perfect Focus 3 (PFS3), 100x oil immersion objective (PH3, numerical aperture = 1.45), and Obis laser 488LX(Coherent Inc., CA) as a fluorescence light source, and an Andor NEO sCMOS (Andor Technology) camera. The laser power was 18 mW. The exposure time was 200 ms for phase contrast imaging and 50 ms for fluorescence.

### Experimental conditions

`Strain` *E. coli* MG1655 F- λ- rph-1 DnaN-Ypet (kanamycin resistant)

`Growth medium` MOPS 0.4% glycerol + 11 amino acids. See reference for detailed media recipe.

`Temperature` 37C

### Publications associated with this dataset

**Original publication**

...