Data for: Tools and methods for high-throughput single-cell imaging with the mother machine
Data files
Mar 20, 2024 version files 49.30 GB
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20171225_FS104_gly11a001.nd2
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README.md
Abstract
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 of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, “what you put is what you get” (WYPIWYG) - i.e., pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother-machine-based high-throughput imaging and analysis methods in their research.
README: 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
Fangwei Si, Guillaume Le Treut, John T. Sauls, Stephen Vadia, Petra Anne Levin, Suckjoon Jun. Mechanistic Origin of Cell-Size Control and Homeostasis in Bacteria. Current Biology. Volume 29, Issue 11, 2019, Pages 1760-1770.e7. ISSN 0960-9822.
https://doi.org/10.1016/j.cub.2019.04.062.
Secondary publication
The dataset was reanalyzed in:
Ryan Thiermann, Michael Sandler, Gursharan Ahir, John T. Sauls, Jeremy W. Schroeder, Steven D. Brown, Guillaume Le Treut, Fangwei Si, Dongyang Li, Jue D. Wang, Suckjoon Jun. 2023. Tools and methods for high-throughput single-cell imaging with the mother machine. eLife12:RP88463.
https://doi.org/10.7554/eLife.88463.2
Processed data from this reference is available at the GitHub link in the Related Works section.
Methods
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.