BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology

Abstract

The study of prokaryotic model species has greatly contributed to the advancement of cell biology. Originally viewed as simple organisms lacking internal structure, prokaryotes are now acknowledged to display an impressive degree of subcellular organization (Shapiro et al., 2009). A central question in cell biology is how cells spatiotemporally regulate the positioning and activities of (macro)molecular complexes in order to grow, divide, and adequately respond to changes in their extracellular environment. Studies in established prokaryotic model organisms, such as Bacillus subtilis, Escherichia coli, Caulobacter crescentus, and Vibrio cholerae, have yielded important insights into the mechanisms that organize prokaryotic cells. However, these species only represent a small part of the highly diverse prokaryotic world. Therefore, it is not surprising that the analysis of less commonly studied model species has recently uncovered a series of novel cell-biological pathways (Eswara and Ramamurthi, 2017; Caccamo and Brun, 2018). These findings have significantly

Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans

“…6A and B) and acetate (Fig. 6C and D) at 2-h intervals and subjected the images to automated analysis (10) to determine the average fluorescence per cell (Fig. 6A and C).…”

“…At the indicated time points, the cultures were sampled and analyzed microscopically. Images were subjected to automated analysis using BacStalk (10). (A and C) Distribution of cellular fluorescence intensities ( n = 450 cells per time point) shown as box plots.…”

“…For time-lapse imaging, cells were transferred to a B04 CellASIC ONIX2 microfluidic plate (Merck, Germany) coupled to an ONIX EV262 microfluidic platform (CellASIC, USA), cultivated at 30°C under continuous medium flow (1 lb/in 2 ) and imaged at regular intervals using the microscope setup described above. For automated data analysis, images were processed with Fiji (32) and BacStalk (10).…”

BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data

“…To make BactMAP as useful as possible for the bacterial cell biology community, we standardized the import of datasets from five popular segmentation programs and one single‐molecule tracking program: SuperSegger (Stylianidou et al, ), MicrobeJ (Ducret et al, ), Oufti (Paintdakhi et al, ), Morphometrics (Ursell et al, ), ObjectJ/ChainTracer (Syvertsson, Vischer, Gao, & Hamoen, ; Vischer et al, ) and iSBatch (Caldas, Punter, Ghodke, Robinson, & Oijen, ). Furthermore, new programs with improved or specialized cell segmentation capabilities are being developed constantly, as recently for instance BacStalk (Hartmann, van Teeseling, Thanbichler, & Drescher, ), a specialized tool for segmentation of cells with complex morphologies and the deep learning and machine‐learningbased segmentation programs DeepCell (Bannon et al, ), DeLTA (Lugagne, Lin, & Dunlop, ) and Ilastik (Berg et al, ). Therefore, to make BactMAP compatible with a wide range of current and future segmentation software packages, we also implemented a generic import function for segmentation input.…”

A gradient‐forming MipZ protein mediating the control of cell division in the magnetotactic bacterium Magnetospirillum gryphiswaldense

“…Structural models of proteins were generated with I‐TASSER (Zhang, ) using MipZ Cc as a template and analyzed with the UCSF Chimera package (Pettersen et al , ). Cell length measurements were performed with Fiji (Schindelin et al , ) or BacStalk (Hartmann et al , ). Boxplots were generated using R version 3.5.1 (http://www.r-project.org).…”