scholarly journals Quantifying cellular interaction dynamics in 3D fluorescence microscopy data

2009 ◽  
Vol 4 (9) ◽  
pp. 1305-1311 ◽  
Author(s):  
Frederick Klauschen ◽  
Masaru Ishii ◽  
Hai Qi ◽  
Marc Bajénoff ◽  
Jackson G Egen ◽  
...  
PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260509
Author(s):  
Dennis Eschweiler ◽  
Malte Rethwisch ◽  
Mareike Jarchow ◽  
Simon Koppers ◽  
Johannes Stegmaier

Automated image processing approaches are indispensable for many biomedical experiments and help to cope with the increasing amount of microscopy image data in a fast and reproducible way. Especially state-of-the-art deep learning-based approaches most often require large amounts of annotated training data to produce accurate and generalist outputs, but they are often compromised by the general lack of those annotated data sets. In this work, we propose how conditional generative adversarial networks can be utilized to generate realistic image data for 3D fluorescence microscopy from annotation masks of 3D cellular structures. In combination with mask simulation approaches, we demonstrate the generation of fully-annotated 3D microscopy data sets that we make publicly available for training or benchmarking. An additional positional conditioning of the cellular structures enables the reconstruction of position-dependent intensity characteristics and allows to generate image data of different quality levels. A patch-wise working principle and a subsequent full-size reassemble strategy is used to generate image data of arbitrary size and different organisms. We present this as a proof-of-concept for the automated generation of fully-annotated training data sets requiring only a minimum of manual interaction to alleviate the need of manual annotations.


2017 ◽  
Vol 26 (10) ◽  
pp. 4856-4870 ◽  
Author(s):  
Martin Storath ◽  
Dennis Rickert ◽  
Michael Unser ◽  
Andreas Weinmann

PLoS Genetics ◽  
2020 ◽  
Vol 16 (12) ◽  
pp. e1009246
Author(s):  
Johana Luhur ◽  
Helena Chan ◽  
Benson Kachappilly ◽  
Ahmed Mohamed ◽  
Cécile Morlot ◽  
...  

How organisms develop into specific shapes is a central question in biology. The maintenance of bacterial shape is connected to the assembly and remodelling of the cell envelope. In endospore-forming bacteria, the pre-spore compartment (the forespore) undergoes morphological changes that result in a spore of defined shape, with a complex, multi-layered cell envelope. However, the mechanisms that govern spore shape remain poorly understood. Here, using a combination of fluorescence microscopy, quantitative image analysis, molecular genetics and transmission electron microscopy, we show that SsdC (formerly YdcC), a poorly-characterized new member of the MucB / RseB family of proteins that bind lipopolysaccharide in diderm bacteria, influences spore shape in the monoderm Bacillus subtilis. Sporulating cells lacking SsdC fail to adopt the typical oblong shape of wild-type forespores and are instead rounder. 2D and 3D-fluorescence microscopy suggest that SsdC forms a discontinuous, dynamic ring-like structure in the peripheral membrane of the mother cell, near the mother cell proximal pole of the forespore. A synthetic sporulation screen identified genetic relationships between ssdC and genes involved in the assembly of the spore coat. Phenotypic characterization of these mutants revealed that spore shape, and SsdC localization, depend on the coat basement layer proteins SpoVM and SpoIVA, the encasement protein SpoVID and the inner coat protein SafA. Importantly, we found that the ΔssdC mutant produces spores with an abnormal-looking cortex, and abolishing cortex synthesis in the mutant largely suppresses its shape defects. Thus, SsdC appears to play a role in the proper assembly of the spore cortex, through connections to the spore coat. Collectively, our data suggest functional diversification of the MucB / RseB protein domain between diderm and monoderm bacteria and identify SsdC as an important factor in spore shape development.


Author(s):  
Sven-Thomas Antoni ◽  
Omar M. F. Ismail ◽  
Daniel Schetelig ◽  
Björn-Philipp Diercks ◽  
René Werner ◽  
...  

2001 ◽  
Author(s):  
Alain Dieterlen ◽  
Marie-Pierre Gramain ◽  
Chengqi Xu ◽  
Francois H. Guillemin ◽  
Serge Jacquey

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