scholarly journals Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

2020 ◽  
Author(s):  
Erod Keaton Baybay ◽  
Eric Esposito ◽  
Silke Hauf
Keyword(s):  
Image Analysis ◽  
Fission Yeast ◽  
Three Dimensional ◽  
Cell Types ◽  
Cell Diameter ◽  
Source Image ◽  
A Cell ◽  
Third Dimension ◽  
Microscopy Images ◽  
Classical Size

AbstractThree-dimensional (3D) segmentation of cells in microscopy images is crucial to accurately capture signals that extend across optical sections. Using brightfield images for segmentation has the advantage of being minimally phototoxic and leaving all other channels available for signals of interest. However, brightfield images only readily provide information for two-dimensional (2D) segmentation. In radially symmetric cells, such as fission yeast and many bacteria, this 2D segmentation can be computationally extruded into the third dimension. However, current methods typically make the simplifying assumption that cells are straight rods. Here, we report Pomegranate, a pipeline that performs the extrusion into 3D using spheres placed along the topological skeletons of the 2D-segmented regions. The diameter of these spheres adapts to the cell diameter at each position. Thus, Pomegranate accurately represents radially symmetric cells in 3D even if cell diameter varies and regardless of whether a cell is straight, bent or curved. We have tested Pomegranate on fission yeast and demonstrate its ability to 3D segment wild-type cells as well as classical size and shape mutants. The pipeline is available as macro for the open-source image analysis software Fiji/ImageJ. 2D segmentations created within or outside Pomegranate can serve as input, thus making this a valuable extension to the image analysis portfolio already available for fission yeast and other radially symmetric cell types.

scholarly journals Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Erod Keaton Baybay ◽  
Eric Esposito ◽  
Silke Hauf
Keyword(s):  
Image Analysis ◽  
Fission Yeast ◽  
Three Dimensional ◽  
Cell Types ◽  
Cell Diameter ◽  
Source Image ◽  
A Cell ◽  
Third Dimension ◽  
Microscopy Images ◽  
Classical Size

Abstract Three-dimensional (3D) segmentation of cells in microscopy images is crucial to accurately capture signals that extend across optical sections. Using brightfield images for segmentation has the advantage of being minimally phototoxic and leaving all other channels available for signals of interest. However, brightfield images only readily provide information for two-dimensional (2D) segmentation. In radially symmetric cells, such as fission yeast and many bacteria, this 2D segmentation can be computationally extruded into the third dimension. However, current methods typically make the simplifying assumption that cells are straight rods. Here, we report Pomegranate, a pipeline that performs the extrusion into 3D using spheres placed along the topological skeletons of the 2D-segmented regions. The diameter of these spheres adapts to the cell diameter at each position. Thus, Pomegranate accurately represents radially symmetric cells in 3D even if cell diameter varies and regardless of whether a cell is straight, bent or curved. We have tested Pomegranate on fission yeast and demonstrate its ability to 3D segment wild-type cells as well as classical size and shape mutants. The pipeline is available as a macro for the open-source image analysis software Fiji/ImageJ. 2D segmentations created within or outside Pomegranate can serve as input, thus making this a valuable extension to the image analysis portfolio already available for fission yeast and other radially symmetric cell types.

scholarly journals Quantitative analysis of subcellular distributions with an open-source, object-based tool

Biology Open ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. bio055228 ◽  
Author(s):  
Pearl V. Ryder ◽  
Dorothy A. Lerit
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Three Dimensional ◽  
Analysis Data ◽  
Form And Function ◽  
Object Based Image Analysis ◽  
Object Based ◽  
And Function ◽  
Microscopy Images ◽  
Complete Process

ABSTRACTThe subcellular localization of objects, such as organelles, proteins, or other molecules, instructs cellular form and function. Understanding the underlying spatial relationships between objects through colocalization analysis of microscopy images is a fundamental approach used to inform biological mechanisms. We generated an automated and customizable computational tool, the SubcellularDistribution pipeline, to facilitate object-based image analysis from three-dimensional (3D) fluorescence microcopy images. To test the utility of the SubcellularDistribution pipeline, we examined the subcellular distribution of mRNA relative to centrosomes within syncytial Drosophila embryos. Centrosomes are microtubule-organizing centers, and RNA enrichments at centrosomes are of emerging importance. Our open-source and freely available software detected RNA distributions comparably to commercially available image analysis software. The SubcellularDistribution pipeline is designed to guide the user through the complete process of preparing image analysis data for publication, from image segmentation and data processing to visualization.This article has an associated First Person interview with the first author of the paper.

A NIMA homologue promotes chromatin condensation in fission yeast

1998 ◽  
Vol 111 (7) ◽  
pp. 967-976 ◽  
Author(s):  
M.J. Krien ◽  
S.J. Bugg ◽  
M. Palatsides ◽  
G. Asouline ◽  
M. Morimyo ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Fission Yeast ◽  
Chromatin Condensation ◽  
Cell Types ◽  
Cell Cycle Delay ◽  
Downstream Target ◽  
A Cell ◽  
Chromatin Organisation ◽  
Bona Fide ◽  
P34 Cdc2

Entry into mitosis requires p34(cdc2), which activates downstream mitotic events through phosphorylation of key target proteins. In Aspergillus nidulans, the NIMA protein kinase has been identified as a potential downstream target and plays a role in regulating chromatin condensation at mitosis. nimA- mutants arrest in a state that physically resembles interphase even though p34(cdc2) is fully active. Despite evidence for the existence of NIMA-like activities in a variety of cell types, the only bona fide NIMA homologue that has been identified is the nim-1 gene of Neurospora crassa. We report here the isolation of a fission yeast NIMA homologue, and have designated this gene fin1 and the 83 kDa predicted protein p83(fin1). Overexpression of fin1 promotes premature chromatin condensation from any point in the cell cycle independently of p34(cdc2) function. Like NIMA, p83(fin1) levels fluctuate through the cell cycle, peaking in mitosis and levels are greatly elevated by removal of C-terminal PEST sequences. Deletion of fin1 results in viable but elongated cells, indicative of a cell cycle delay. Genetic analysis has placed this delay in G2 but, unlike in nimA mutants of Aspergillus, p34(cdc2) activation appears to be delayed. Interaction of fin1 mutants with other strains defective in chromatin organisation also support the hypothesis of p83(fin1) playing a role in this process at the onset of mitosis. These data indicate that NIMA-related kinases may be a general feature of the cell cycle and chromatin organisation at mitosis.

scholarly journals Spatial protein analysis in developing tissues: a sampling-based image processing approach

2020 ◽  
Vol 375 (1809) ◽  
pp. 20190560 ◽  
Author(s):  
Karolis Leonavicius ◽  
Christophe Royer ◽  
Antonio M. A. Miranda ◽  
Richard C. V. Tyser ◽  
Annemarie Kip ◽  
...  
Keyword(s):  
Image Analysis ◽  
Web Application ◽  
Protein Localization ◽  
Three Dimensional ◽  
Embryonic Stem ◽  
Quantitative Information ◽  
Embryoid Bodies ◽  
Source Image ◽  
Protein Distribution ◽  
Tissue Geometry

Advances in fluorescence microscopy approaches have made it relatively easy to generate multi-dimensional image volumes and have highlighted the need for flexible image analysis tools for the extraction of quantitative information from such data. Here we demonstrate that by focusing on simplified feature-based nuclear segmentation and probabilistic cytoplasmic detection we can create a tool that is able to extract geometry-based information from diverse mammalian tissue images. Our open-source image analysis platform, called ‘SilentMark’, can cope with three-dimensional noisy images and with crowded fields of cells to quantify signal intensity in different cellular compartments. Additionally, it provides tissue geometry related information, which allows one to quantify protein distribution with respect to marked regions of interest. The lightweight SilentMark algorithms have the advantage of not requiring multiple processors, graphics cards or training datasets and can be run even with just several hundred megabytes of memory. This makes it possible to use the method as a Web application, effectively eliminating setup hurdles and compatibility issues with operating systems. We test this platform on mouse pre-implantation embryos, embryonic stem cell-derived embryoid bodies and mouse embryonic heart, and relate protein localization to tissue geometry. This article is part of a discussion meeting issue ‘Contemporary morphogenesis’.

scholarly journals Golgi Enzymes Are Enriched in Perforated Zones of Golgi Cisternae but Are Depleted in COPI Vesicles

2004 ◽  
Vol 15 (10) ◽  
pp. 4710-4724 ◽  
Author(s):  
Hee-Seok Kweon ◽  
Galina V. Beznoussenko ◽  
Massimo Micaroni ◽  
Roman S. Polishchuk ◽  
Alvar Trucco ◽  
...  
Keyword(s):  
Golgi Complex ◽  
Three Dimensional ◽  
Retrograde Transport ◽  
Cell Types ◽  
Free System ◽  
Progression Model ◽  
Golgi Transport ◽  
A Cell ◽  
Different Cell Types

In the most widely accepted version of the cisternal maturation/progression model of intra-Golgi transport, the polarity of the Golgi complex is maintained by retrograde transport of Golgi enzymes in COPI-coated vesicles. By analyzing enzyme localization in relation to the three-dimensional ultrastructure of the Golgi complex, we now observe that Golgi enzymes are depleted in COPI-coated buds and 50- to 60-nm COPI-dependent vesicles in a variety of different cell types. Instead, we find that Golgi enzymes are concentrated in the perforated zones of cisternal rims both in vivo and in a cell-free system. This lateral segregation of Golgi enzymes is detectable in some stacks during steady-state transport, but it was significantly prominent after blocking endoplasmic reticulum-to-Golgi transport. Delivery of transport carriers to the Golgi after the release of a transport block leads to a diminution in Golgi enzyme concentrations in perforated zones of cisternae. The exclusion of Golgi enzymes from COPI vesicles and their transport-dependent accumulation in perforated zones argues against the current vesicle-mediated version of the cisternal maturation/progression model.

scholarly journals CellProfiler 4: Improvements in Speed, Utility and Usability

2021 ◽  
Author(s):  
David R Stirling ◽  
Madison J Swain-Bowden ◽  
Alice M Lucas ◽  
Anne E. Carpenter ◽  
Beth A Cimini ◽  
...  
Keyword(s):  
Image Analysis ◽  
User Interface ◽  
Large Scale ◽  
Source Image ◽  
Scale Analysis ◽  
Analysis Program ◽  
Computational Tools ◽  
Large Scale Analysis ◽  
Free Open Source ◽  
Microscopy Images

CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Here we describe CellProfiler 4, a new version of this software which has been ported to the Python 3 language. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimisations to reduce the time and cost associated with running common large-scale analysis pipelines. This release will ensure that researchers will have continued access to CellProfilers powerful computational tools in the coming years.

Imaging the Cell's Third Dimension

2012 ◽  
Vol 20 (3) ◽  
pp. 32-37 ◽  
Author(s):  
Michael A. Model
Keyword(s):  
Vertical Profile ◽  
Three Dimensional ◽  
Image Plane ◽  
Physical Object ◽  
Fluorescent Labeling ◽  
Ion Conductance ◽  
Force Microscopy ◽  
Atomic Force ◽  
A Cell ◽  
Third Dimension

Shape and size are among the most basic and obvious characteristics of a cell (or of any physical object, for that matter). When a cell is observed through a microscope, one only sees its projection onto the image plane. Rather paradoxically, there are no easy techniques to visualize and measure cell's third dimension—thickness. For example, confocal microscopy requires fluorescent labeling, multiple scanning with a high-power objective, possibly correction for the refractive index mismatch, and even then, generation of a complete three-dimensional profile is not very straightforward or precise. Other techniques for imaging the cell vertical profile, such as ion conductance, digital holographic, or atomic force microscopy, are rather complex and not available to most users.

Three-Dimensional Reconstruction of Murine Peyer's Patches from Immunostained Cryosections

2013 ◽  
Vol 20 (1) ◽  
pp. 198-205 ◽  
Author(s):  
Sarita Ahlawat ◽  
Magdia De Jesus ◽  
Kedar Khare ◽  
Richard A. Cole ◽  
Nicholas J. Mantis
Keyword(s):  
Three Dimensional ◽  
Cell Types ◽  
Peyer's Patches ◽  
Source Image ◽  
Peyer’S Patches ◽  
Peyer’S Patch ◽  
Peyer's Patch ◽  
Lymphoid Follicles ◽  
Dimensional Reconstruction ◽  
Specialized Tissue

AbstractPeyer's patches, macroscopic aggregates of lymphoid follicles present throughout the small intestines of humans and other mammals, are considered the gateway through which luminal dietary antigens and microbes are sampled by the mucosal immune system. The cellular make-up of Peyer's patch lymphoid follicles is not only complex, but highly dynamic, as there are at least four major cell types that are known to migrate in response to antigenic stimulation. In an effort to capture the complexity and dynamic nature of this specialized tissue, here we report the three-dimensional (3D) reconstruction of immunofluorescent-labeled mouse Peyer's patch cryosections. The technology that enabled the stacking and linear blending of serial cryosections was a novel macro for Fiji, the open source image-processing package based on ImageJ. By simultaneously labeling cryosections for surface markers CD45R, CD3, and CD11c, we provide a 3D image as well as quantitative measures of B-cell, T-cell, and dendritic cell populations at steady state and following exposure to the mucosal adjuvant cholera toxin.

scholarly journals Force-based three-dimensional model predicts mechanical drivers of cell sorting

2018 ◽  
Author(s):  
Christopher Revell ◽  
Raphael Blumenfeld ◽  
Kevin Chalut
Keyword(s):  
Cell Sorting ◽  
Three Dimensional ◽  
Theoretical Work ◽  
Simulation Method ◽  
Cell Types ◽  
Cell Cortex ◽  
Biological Processes ◽  
Three Dimensional Model ◽  
Multicellular Aggregates ◽  
A Cell

AbstractMany biological processes, including tissue morphogenesis, are driven by mechanical sorting. However, the primary mechanical drivers of cell sorting remain controversial, in part because there remains a lack of appropriate threedimensional computational methods to probe the mechanical interactions that drive sorting. To address this important issue, we developed a three-dimensional, local force-based simulation method to enable such investigation into the sorting mechanisms of multicellular aggregates. Our method utilises the subcellular element method, in which cells are modeled as collections of locally-interacting force-bearing elements, accommodating cell growth and cell division. We define two different types of intracellular elements, assigning different attributes to boundary elements to model a cell cortex, which mediates the interfacial interaction between different cells. By tuning interfacial adhesion and tension in each cell cortex, we can control and predict the degree of sorting in cellular aggregates. The method is validated by comparing the interface areas of simulated cell doublets to experimental data and to previous theoretical work. We then define numerical measures of sorting and investigate the effects of mechanical parameters on the extent of sorting in multicellular aggregates. Using this method, we find that a minimum adhesion is required for differential interfacial tension to produce inside-out sorting of two cell types with different mechanical phenotypes. We predict the value of the minimum adhesion, which is in excellent agreement with observations in several developmental systems. We also predict the level of tension asymmetry needed for robust sorting. The generality and flexibility of the method make it applicable to tissue self-organization in a myriad of biological processes, such as tumorigenesis and embryogenesis.

Adult, foetal and transformed fibroblasts display different migratory phenotypes on collagen gels: evidence for an isoformic transition during foetal development

1985 ◽  
Vol 73 (1) ◽  
pp. 221-234 ◽  
Author(s):  
S.L. Schor ◽  
A.M. Schor ◽  
G. Rushton ◽  
L. Smith
Keyword(s):  
Cell Density ◽  
Three Dimensional ◽  
Cell Types ◽  
Normal Adult ◽  
Transformed Cells ◽  
Collagen Gels ◽  
Foetal Development ◽  
A Cell ◽  
Transformed Cell Lines

Data are presented indicating that the migration of fibroblasts into three-dimensional collagen gels is affected by cell density. We have defined a ‘cell density migration index’ (CDMI) to express this behavioural response in quantitative terms. The results of a survey of 77 different cell types indicate that the CDMI values expressed by normal adult skin fibroblasts and transformed cell lines fall into two distinct, non-overlapping groups. Measurement of the CDMI therefore provides an additional means of distinguishing between normal and transformed cells and may be used in conjunction with other commonly recognized criteria (e.g. anchorage-independent growth) to assess expression of a transformed phenotype in vitro. It is of interest to note that the CDMI values expressed by foetal cells define a group lying intermediate between normal and transformed cells. Both uncloned and cloned foetal cells have been observed to undergo a stable transition to expression of CDMI values characteristic of adult cells when followed throughout the duration of their in vitro lifespan. In addition to providing a novel means of distinguishing between normal adult and foetal cells, our results suggest that foetal fibroblasts undergo an ‘isoformic’ transition at some point in their developmental history, which is manifest in vitro by the expression of an adult CDMI.

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