scholarly journals Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells

2021 ◽  
Vol 7 (6) ◽  
pp. 93
Author(s):  
Cefa Karabağ ◽  
Martin L. Jones ◽  
Constantino Carlos Reyes-Aldasoro
Keyword(s):  
Plasma Membrane ◽  
Hela Cells ◽  
Similarity Index ◽  
Ground Truth ◽  
Regions Of Interest ◽  
Distance Map ◽  
Block Face ◽  
Processing Steps ◽  
Instance Segmentation ◽  
Traditional Image

In this work, an unsupervised volumetric semantic instance segmentation of the plasma membrane of HeLa cells as observed with serial block face scanning electron microscopy is described. The resin background of the images was segmented at different slices of a 3D stack of 518 slices with 8192 × 8192 pixels each. The background was used to create a distance map, which helped identify and rank the cells by their size at each slice. The centroids of the cells detected at different slices were linked to identify them as a single cell that spanned a number of slices. A subset of these cells, i.e., the largest ones and those not close to the edges were selected for further processing. The selected cells were then automatically cropped to smaller regions of interest of 2000 × 2000 × 300 voxels that were treated as cell instances. Then, for each of these volumes, the nucleus was segmented, and the cell was separated from any neighbouring cells through a series of traditional image processing steps that followed the plasma membrane. The segmentation process was repeated for all the regions of interest previously selected. For one cell for which the ground truth was available, the algorithm provided excellent results in Accuracy (AC) and the Jaccard similarity Index (JI): nucleus: JI =0.9665, AC =0.9975, cell including nucleus JI =0.8711, AC =0.9655, cell excluding nucleus JI =0.8094, AC =0.9629. A limitation of the algorithm for the plasma membrane segmentation was the presence of background. In samples with tightly packed cells, this may not be available. When tested for these conditions, the segmentation of the nuclear envelope was still possible. All the code and data were released openly through GitHub, Zenodo and EMPIAR.

scholarly journals Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells

2021 ◽  
Author(s):  
Cefa Karabağ ◽  
Martin L. Jones ◽  
Constantino Carlos Reyes-Aldasoro
Keyword(s):  
Plasma Membrane ◽  
Hela Cells ◽  
Ground Truth ◽  
Semantic Segmentation ◽  
Distance Map ◽  
Block Face ◽  
Processing Steps ◽  
Membrane Segmentation ◽  
Instance Segmentation ◽  
Traditional Image

In this work, the unsupervised volumetric semantic segmentation of the plasma membrane of HeLa cells as observed with Serial Block Face Scanning Electron Microscopy is described. The resin background of the images was segmented at different slices of a 3D stack of 518 slices with 8, 192 x 8, 192 pixels each. The background was used to create a distance map which helped identify and rank the cells by their size at each slice. The centroids of the cells detected at different slices were linked to identify them as a single cell that spanned a number of slices. A subset of these cells, i.e., largest ones and those not close to the edges were selected for further processing. The selected cells were then automatically cropped to smaller regions of interest of 2, 000 x 2, 000 x 300 voxels that were treated as cell instances. Then, for each of these volumes the nucleus was segmented and the cell was separated from any neighbouring cells through a series of traditional image processing steps that followed the plasma membrane. The segmentation process was repeated for all the regions selected. For one cell for which the ground truth was available, the algorithm provided excellent results in Accuracy (AC) and Jaccard Index (JI): Nucleus: JI = 0.9665, AC= 0.9975, Cell and Nucleus JI = 0.8711, AC = 0.9655, Cell only JI = 0.8094, AC = 0.9629. A limitation of the algorithm for the plasma membrane segmentation was the presence of background, as in cases of tightly packed cells. When tested for these conditions, the segmentation of the nuclear envelope was still possible. All the code and data are released openly through GitHub, Zenodo and EMPIAR.

scholarly journals Fully Data-Driven Pseudohealthy Synthesis for Planning Valve-Sparing Aortic Root Reconstruction using Conditional Variational Autoencoders

2020 ◽  
Vol 6 (3) ◽  
pp. 284-287
Author(s):  
Jannis Hagenah ◽  
Mohamad Mehdi ◽  
Floris Ernst
Keyword(s):  
Aortic Root ◽  
Similarity Index ◽  
Ground Truth ◽  
Representation Learning ◽  
Patient Specific ◽  
Ultrasound Images ◽  
Specific Geometry ◽  
The Individual ◽  
Native Root ◽  
Original Information

AbstractAortic root aneurysm is treated by replacing the dilated root by a grafted prosthesis which mimics the native root morphology of the individual patient. The challenge in predicting the optimal prosthesis size rises from the highly patient-specific geometry as well as the absence of the original information on the healthy root. Therefore, the estimation is only possible based on the available pathological data. In this paper, we show that representation learning with Conditional Variational Autoencoders is capable of turning the distorted geometry of the aortic root into smoother shapes while the information on the individual anatomy is preserved. We evaluated this method using ultrasound images of the porcine aortic root alongside their labels. The observed results show highly realistic resemblance in shape and size to the ground truth images. Furthermore, the similarity index has noticeably improved compared to the pathological images. This provides a promising technique in planning individual aortic root replacement.

scholarly journals Entry of the Two Infectious Forms of Vaccinia Virus at the Plasma Membane Is Signaling-Dependent for the IMV but Not the EEV

2000 ◽  
Vol 11 (7) ◽  
pp. 2497-2511 ◽  
Author(s):  
Jacomine Krijnse Locker ◽  
Annett Kuehn ◽  
Sibylle Schleich ◽  
Gaby Rutter ◽  
Heinrich Hohenberg ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Protein Kinase C ◽  
Protein Kinase ◽  
Cell Surface ◽  
Vaccinia Virus ◽  
Hela Cells ◽  
Signaling Cascade ◽  
Enveloped Virus ◽  
Kinase C ◽  
Mature Virus

The simpler of the two infectious forms of vaccinia virus, the intracellular mature virus (IMV) is known to infect cells less efficiently than the extracellular enveloped virus (EEV), which is surrounded by an additional, TGN-derived membrane. We show here that when the IMV binds HeLa cells, it activates a signaling cascade that is regulated by the GTPase rac1 and rhoA, ezrin, and both tyrosine and protein kinase C phosphorylation. These cascades are linked to the formation of actin and ezrin containing protrusions at the plasma membrane that seem to be essential for the entry of IMV cores. The identical cores of the EEV also appear to enter at the cell surface, but surprisingly, without the need for signaling and actin/membrane rearrangements. Thus, in addition to its known role in wrapping the IMV and the formation of intracellular actin comets, the membrane of the EEV seems to have evolved the capacity to enter cells silently, without a need for signaling.

Ability to organize microtubules in taxol-treated mitotic PtK2 cells goes with the SPN antigen and not with the centrosome

1992 ◽  
Vol 102 (1) ◽  
pp. 91-102 ◽  
Author(s):  
M. Kallajoki ◽  
K. Weber ◽  
M. Osborn
Keyword(s):  
Plasma Membrane ◽  
Hela Cells ◽  
Nuclear Matrix ◽  
Essential Role ◽  
Soluble Form ◽  
Microtubule Nucleation ◽  
Brain Microtubules ◽  
Mitotic Cells

The SPN antigen plays an essential role in mitosis, since microinjection of antibodies causes mitotic arrest. Here we show, by examination of the relative locations of SPN antigen, the centrosomal 5051 antigen and tubulin in normal mitotic, and in taxol-treated mitotic cells, that the SPN antigen is involved in organizing the microtubules of the spindle. The 210 kDa protein defined as SPN antigen relocates from the nuclear matrix to the centrosome at prophase, remains associated with the poles at metaphase and anaphase, and dissociates from the centrosomes in telophase. In taxol-treated mitotic cells, SPN staining shows a striking redistribution while 5051 antigen remains associated with centrosomes. SPN antigen is seen at the plasma membrane end of the rearranged microtubules. SPN antigen is always at the center of the multiple microtubule asters (5 to 20 per cell) induced by taxol, whereas 5051 again remains associated with the centrosomal complex (1 to 2 foci per cell). Microtubule nucleation is associated with the SPN antigen rather than with the 5051 antigen. Microinjection of SPN-3 antibody into taxol-treated mitotic PtK2 cells causes disruption of the asters as judged by tubulin staining of the same cells. Finally, SPN antigen extracted in soluble form from synchronized mitotic HeLa cells binds to, and sediments with, pig brain microtubules stabilized by taxol. This association of SPN antigen with microtubules is partially dissociated by 0.5 M NaCl but not by 5 mM ATP. Thus SPN antigen binds to microtubules in vitro and seems to act as a microtubular minus-end organizer in mitotic cells in vivo.

Thermal transitions in the adhesiveness of HeLa cells: effects of cell growth, trypsin treatment and calcium

1977 ◽  
Vol 27 (1) ◽  
pp. 167-181
Author(s):  
J.J. Deman ◽  
E.A. Bruyneel
Keyword(s):  
Phase Transition ◽  
Plasma Membrane ◽  
Hela Cells ◽  
Membrane Lipids ◽  
Previous Treatment ◽  
Membrane Glycoproteins ◽  
Thermal Transitions ◽  
Fluorescent Compound ◽  
Fast Growing ◽  
Buffer Medium

The intercellular adhesiveness of density-inhibited (D.I.) and fast-growing (F.G.) HeLa cells and of trypsin-treated preparations of these, has been measured at temperatures between 37 and 6 degrees C. In EDTA-containing buffer medium, F.G. cells differ from D.I. cells in that only the former display an increase in adhesiveness below 30 degrees C. This increase is prevented by previous treatment with trypsin. The presence of Ca2+ in the buffer medium causes a narrowing of the thermal transition region of intact F.G. cells. On intact D.I. cells Ca2+ causes an increase in adhesiveness at temperatures below 20 degrees C. Previous trypsinization of F.G. cells diminishes the effect of subsequent Ca2+ addition. The adhesiveness of trypsinized D.I. cells is indifferent to changes in temperature in Ca2+-containing buffer medium. The results are considered evidence for the occurrence of a phase transition in the glycoprotein domains of the plasma membrane of fast-growing cells. The transition is influenced by growth rate, trypsinization and Ca2+. The fluidity of the membrane glycoproteins is considered to be higher on density-inhibited cells than on fast-growing cells. No phase transition could be detected after incorporation of the fluorescent compound 1,6-diphenyl 1,3,5-hexatriene into the lipid domain of the plasma membrane. The fluidity of the membrane lipids is lower on density-inhibited cells than on fast-growing cells.

scholarly journals SOGNet: Scene Overlap Graph Network for Panoptic Segmentation

2020 ◽  
Vol 34 (07) ◽  
pp. 12637-12644 ◽  
Author(s):  
Yibo Yang ◽  
Hongyang Li ◽  
Xia Li ◽  
Qijie Zhao ◽  
Jianlong Wu ◽  
...  
Keyword(s):  
State Of The Art ◽  
Ground Truth ◽  
The State ◽  
Graph Representation ◽  
Weak Supervision ◽  
Scene Graph ◽  
Art Performance ◽  
Segmentation Task ◽  
Instance Segmentation ◽  
Relation Matrix

The panoptic segmentation task requires a unified result from semantic and instance segmentation outputs that may contain overlaps. However, current studies widely ignore modeling overlaps. In this study, we aim to model overlap relations among instances and resolve them for panoptic segmentation. Inspired by scene graph representation, we formulate the overlapping problem as a simplified case, named scene overlap graph. We leverage each object's category, geometry and appearance features to perform relational embedding, and output a relation matrix that encodes overlap relations. In order to overcome the lack of supervision, we introduce a differentiable module to resolve the overlap between any pair of instances. The mask logits after removing overlaps are fed into per-pixel instance id classification, which leverages the panoptic supervision to assist in the modeling of overlap relations. Besides, we generate an approximate ground truth of overlap relations as the weak supervision, to quantify the accuracy of overlap relations predicted by our method. Experiments on COCO and Cityscapes demonstrate that our method is able to accurately predict overlap relations, and outperform the state-of-the-art performance for panoptic segmentation. Our method also won the Innovation Award in COCO 2019 challenge.

scholarly journals Sphingomyelin homeostasis is required to form functional enzymatic domains at the trans-Golgi network

2014 ◽  
Vol 206 (5) ◽  
pp. 609-618 ◽  
Author(s):  
Josse van Galen ◽  
Felix Campelo ◽  
Emma Martínez-Alonso ◽  
Margherita Scarpa ◽  
José Ángel Martínez-Menárguez ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Hela Cells ◽  
Transmembrane Proteins ◽  
Short Chain ◽  
Membrane Domains ◽  
Trans Golgi Network ◽  
And Function ◽  
Golgi Network ◽  
Specific Membrane

Do lipids such as sphingomyelin (SM) that are known to assemble into specific membrane domains play a role in the organization and function of transmembrane proteins? In this paper, we show that disruption of SM homeostasis at the trans-Golgi network (TGN) by treatment of HeLa cells with d-ceramide-C6, which was converted together with phosphatidylcholine to short-chain SM and diacylglycerol by SM synthase, led to the segregation of Golgi-resident proteins from each other. We found that TGN46, which cycles between the TGN and the plasma membrane, was not sialylated by a sialyltransferase at the TGN and that this enzyme and its substrate TGN46 could not physically interact with each other. Our results suggest that SM organizes transmembrane proteins into functional enzymatic domains at the TGN.

Interaction of vaginal Lactobacillus strains with HeLa cells plasma membrane

2017 ◽  
Vol 8 (4) ◽  
pp. 625-633 ◽  
Author(s):  
N. Calonghi ◽  
C. Parolin ◽  
G. Sartor ◽  
L. Verardi ◽  
B. Giordani ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Physical Properties ◽  
Hela Cells ◽  
Protective Role ◽  
Vaginal Infections ◽  
Vaginal Lactobacilli ◽  
Cell Line Hela ◽  
Cervical Cells ◽  
Host Epithelium

Vaginal lactobacilli offer protection against recurrent urinary and vaginal infections. The precise mechanisms underlying the interaction between lactobacilli and the host epithelium remain poorly understood at the molecular level. Deciphering such events can provide valuable information on the mode of action of commensal and probiotic bacteria in the vaginal environment. We investigated the effects exerted by five Lactobacillus strains of vaginal origin (Lactobacillus crispatus BC1 and BC2, Lactobacillus gasseri BC9 and BC11 and Lactobacillus vaginalis BC15) on the physical properties of the plasma membrane in a cervical cell line (HeLa). The interaction of the vaginal lactobacilli with the cervical cells determined two kinds of effects on plasma membrane: (1) modification of the membrane polar lipid organisation and the physical properties (L. crispatus BC1 and L. gasseri BC9); (2) modification of α5β1 integrin organisation (L. crispatus BC2, L. gasseri BC11 and L. vaginalis BC15). These two mechanisms can be at the basis of the protective role of lactobacilli against Candida albicans adhesion. Upon stimulation with all Lactobacillus strains, we observed a reduction of the basal oxidative stress in HeLa cells that could be related to modifications in physical properties and organisation of the plasma membrane. These results confirm the strictly strain-specific peculiarities of Lactobacillus and deepen the understanding of the mechanisms underlying the health-promoting role of this genus within the vaginal ecosystem.

scholarly journals Different consequences of cataract-associated mutations at adjacent positions in the first extracellular boundary of connexin50

2011 ◽  
Vol 300 (5) ◽  
pp. C1055-C1064 ◽  
Author(s):  
Jun-Jie Tong ◽  
Peter J. Minogue ◽  
Wenji Guo ◽  
Tung-Ling Chen ◽  
Eric C. Beyer ◽  
...  
Keyword(s):  
Amino Acids ◽  
Plasma Membrane ◽  
Hela Cells ◽  
Xenopus Oocytes ◽  
Dominant Negative ◽  
Wild Type ◽  
Gap Junction Channels ◽  
Dominant Negative Inhibitor ◽  
Intercellular Channels ◽  
Gap Junctional

Gap junction channels, which are made of connexins, are critical for intercellular communication, a function that may be disrupted in a variety of diseases. We studied the consequences of two cataract-associated mutations at adjacent positions at the first extracellular boundary in human connexin50 (Cx50), W45S and G46V. Both of these mutants formed gap junctional plaques when they were expressed in HeLa cells, suggesting that they trafficked to the plasma membrane properly. However, their functional properties differed. Dual two-microelectrode voltage-clamp studies showed that W45S did not form functional intercellular channels in paired Xenopus oocytes or hemichannel currents in single oocytes. When W45S was coexpressed with wild-type Cx50, the mutant acted as a dominant negative inhibitor of wild-type function. In contrast, G46V formed both functional gap junctional channels and hemichannels. G46V exhibited greatly enhanced currents compared with wild-type Cx50 in the presence of physiological calcium concentrations. This increase in hemichannel activity persisted when G46V was coexpressed with wild-type lens connexins, consistent with a dominant gain of hemichannel function for G46V. These data suggest that although these two mutations are in adjacent amino acids, they have very different effects on connexin function and cause disease by different mechanisms: W45S inhibits gap junctional channel function; G46V reduces cell viability by forming open hemichannels.

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