Cell segmentation based on spatial information improved intuitionistic fcm combined with FOPSO

2017 ◽  
Author(s):  
Chuxiong Sun ◽  
Xiangzhi Bai
Keyword(s):  
Spatial Information ◽  
Cell Segmentation

scholarly journals Spage2vec: Unsupervised detection of spatial gene expression constellations

2020 ◽  
Author(s):  
Gabriele Partel ◽  
Carolina Wählby
Keyword(s):  
Gene Expression ◽  
Spatial Information ◽  
Graph Representation ◽  
Cell Segmentation ◽  
Biological Knowledge ◽  
Unsupervised Segmentation ◽  
Tissue Samples ◽  
Prior Biological Knowledge ◽  
Brain Data

ABSTRACTInvestigation of spatial cellular composition of tissue architectures revealed by multiplexed in situ RNA detection often rely on inaccurate cell segmentation or prior biological knowledge from complementary single cell sequencing experiments. Here we present spage2vec, an unsupervised segmentation free approach for decrypting the spatial transcriptomic heterogeneity of complex tissues at subcellular resolution. Spage2vec represents the spatial transcriptomic landscape of tissue samples as a spatial functional network and leverages a powerful machine learning graph representation technique to create a lower dimensional representation of local spatial gene expression. We apply spage2vec to mouse brain data from three different in situ transcriptomic assays, showing that learned representations encode meaningful biological spatial information of re-occuring gene constellations involved in cellular and subcellular processes.

scholarly journals Deep learning on image-omics data in identifying prognostic immune biomarkers for ovarian cancer

2020 ◽  
Author(s):  
Ying Zhu ◽  
Sammy Ferri-Borgogno ◽  
Jianting Sheng ◽  
Tsz-Lun Yeung ◽  
Jared Burks ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Immune Cells ◽  
Spatial Information ◽  
Survival Rates ◽  
Image Data ◽  
Cell Segmentation ◽  
Sequencing Data ◽  
Prognostic Features ◽  
Immune Biomarkers ◽  
Treatment Naïve

Abstract Although stromal and immune cells in the tumor microenvironment have been shown to directly affect tumor growth and chemoresistance, how the interactions among stromal and immune cells and their spatially resolved cell heterogeneity would influence ovarian patients’ survival remains largely unknown. To fill this gap, we developed a new imageomics method that (i) incorporates an artificial intelligence–based analytics pipeline for imaging mass cytometry (IMC) to increase the accuracy of cell segmentation and spatial information extraction in order to identify immune biomarkers and their interactions that can predict overall survival rates in patients with treatment-naïve ovarian cancer, and (ii) integrates quantitated spatial IMC image data with microdissected tumor and stromal transcriptomic data from the same patients as well as single-cell RNA sequencing data to detect genes correlated with the prognostic features and postulate novel mechanisms by which these genes contribute to the prognostic features.

scholarly journals Quantitative Visualization of Hypoxia and Proliferation Gradients Within Histological Tissue Sections

2019 ◽  
Author(s):  
Mark Zaidi ◽  
Fred Fu ◽  
Dan Cojocari ◽  
Trevor D. McKee ◽  
Bradly G. Wouters
Keyword(s):  
Molecular Mechanisms ◽  
Spatial Information ◽  
Radiation Treatment ◽  
Tumor Hypoxia ◽  
Chemotherapy Resistance ◽  
Cell Segmentation ◽  
Distance Analysis ◽  
Hypoxic Tolerance ◽  
Quantitative Visualization ◽  
Analysis Strategy

AbstractThe formation of hypoxic microenvironments within solid tumors is known to contribute to radiation resistance, chemotherapy resistance, immune suppression, increased metastasis, and an overall poor prognosis. It is therefore crucial to understand the spatial and molecular mechanisms that contribute to tumor hypoxia formation to improve the efficacy of radiation treatment, develop hypoxia-directed therapies, and increase patient survival. The objective of this study is to present a number of complementary novel methods for quantifying tumor hypoxia and proliferation, especially in relation to the location of perfused blood vessels.Multiplexed immunofluorescence staining can produce whole slide scanned image datasets that are amenable for computational pathology analysis. A standard marker analysis strategy is to take a positive pixel count approach, in which a threshold for positive stain is used to compute a positive area fraction for hypoxia. This work is a reassessment of that approach, utilizing not only cell segmentation but also distance to nearest blood vessel in order to incorporate spatial information into the analysis. We describe a reproducible pipeline for the visualization and quantitative analysis of hypoxia using a vessel distance analysis approach. This methodological pipeline can serve to further elucidate the relationship between vessel distance and microenvironment-linked markers such as hypoxia and proliferation, can help to quantify parameters relating to oxygen consumption and hypoxic tolerance in tissues, as well as potentially serve as a hypothesis generating tool for future studies testing hypoxia-linked markers.

scholarly journals Integrated Cells and Collagen Fibers Spatial Image Analysis

2021 ◽  
Vol 1 ◽  
Author(s):  
Georgii Vasiukov ◽  
Tatiana Novitskaya ◽  
Maria-Fernanda Senosain ◽  
Alex Camai ◽  
Anna Menshikh ◽  
...  
Keyword(s):  
Image Analysis ◽  
Spatial Analysis ◽  
Spatial Information ◽  
Fluorescent Microscopy ◽  
Cell Segmentation ◽  
Feature Analysis ◽  
Integrated Analysis ◽  
Dependent Manner ◽  
Structural Patterns ◽  
Cellular Markers

Modern technologies designed for tissue structure visualization like brightfield microscopy, fluorescent microscopy, mass cytometry imaging (MCI) and mass spectrometry imaging (MSI) provide large amounts of quantitative and spatial information about cells and tissue structures like vessels, bronchioles etc. Many published reports have demonstrated that the structural features of cells and extracellular matrix (ECM) and their interactions strongly predict disease development and progression. Computational image analysis methods in combination with spatial analysis and machine learning can reveal novel structural patterns in normal and diseased tissue. Here, we have developed a Python package designed for integrated analysis of cells and ECM in a spatially dependent manner. The package performs segmentation, labeling and feature analysis of ECM fibers, combines this information with pre-generated single-cell based datasets and realizes cell-cell and cell-fiber spatial analysis. To demonstrate performance and compatibility of our computational tool, we integrated it with a pipeline designed for cell segmentation, classification, and feature analysis in the KNIME analytical platform. For validation, we used a set of mouse mammary gland tumors and human lung adenocarcinoma tissue samples stained for multiple cellular markers and collagen as the main ECM protein. The developed package provides sufficient performance and precision to be used as a novel method to investigate cell-ECM relationships in the tissue, as well as detect structural patterns correlated with specific disease outcomes.

Practical Picture Processing

1974 ◽  
Vol 32 ◽  
pp. 338-339
Author(s):  
T. A. Welton
Keyword(s):  
Radiation Damage ◽  
Coherence Length ◽  
Spatial Information ◽  
State Of The Art ◽  
Coherent Radiation ◽  
The State ◽  
Energy Spread ◽  
Electron Micrograph ◽  
Picture Processing ◽  
Molecular Skeleton

Various authors have emphasized the spatial information resident in an electron micrograph taken with adequately coherent radiation. In view of the completion of at least one such instrument, this opportunity is taken to summarize the state of the art of processing such micrographs. We use the usual symbols for the aberration coefficients, and supplement these with £ and 6 for the transverse coherence length and the fractional energy spread respectively. He also assume a weak, biologically interesting sample, with principal interest lying in the molecular skeleton remaining after obvious hydrogen loss and other radiation damage has occurred.

3-D optical transfer in excitation field synthesis microscopes

1995 ◽  
Vol 53 ◽  
pp. 64-65
Author(s):  
Vijay Krishnamurthi ◽  
Brent Bailey ◽  
Frederick Lanni
Keyword(s):  
Standing Wave ◽  
Spatial Information ◽  
3D Structure ◽  
Complete Recovery ◽  
Weighting Factor ◽  
Optical Transfer Function ◽  
Excitation Field ◽  
Optical Transfer ◽  
Set Up ◽  
Focus Plane

Excitation field synthesis (EFS) refers to the use of an interference optical system in a direct-imaging microscope to improve 3D resolution by axially-selective excitation of fluorescence within a specimen. The excitation field can be thought of as a weighting factor for the point-spread function (PSF) of the microscope, so that the optical transfer function (OTF) gets expanded by convolution with the Fourier transform of the field intensity. The simplest EFS system is the standing-wave fluorescence microscope, in which an axially-periodic excitation field is set up through the specimen by interference of a pair of collimated, coherent, s-polarized beams that enter the specimen from opposite sides at matching angles. In this case, spatial information about the object is recovered in the central OTF passband, plus two symmetric, axially-shifted sidebands. Gaps between these bands represent "lost" information about the 3D structure of the object. Because the sideband shift is equal to the spatial frequency of the standing-wave (SW) field, more complete recovery of information is possible by superposition of fields having different periods. When all of the fields have an antinode at a common plane (set to be coincident with the in-focus plane), the "synthesized" field is peaked in a narrow infocus zone.

Use of EDS mapping to characterize thermochemical stability of fibers in intermetallic matrix composites

1992 ◽  
Vol 50 (1) ◽  
pp. 160-161
Author(s):  
John R. Porter
Keyword(s):  
Spatial Information ◽  
Beam Current ◽  
Fiber Types ◽  
Ceramic Fibers ◽  
Dye Transfer ◽  
Science Center ◽  
Commercial Development ◽  
Nih Image ◽  
Intermetallic Matrix Composites ◽  
Thermochemical Stability

New ceramic fibers, currently in various stages of commercial development, have been consolidated in intermetallic matrices such as γ-TiAl and FeAl. Fiber types include SiC, TiB2 and polycrystalline and single crystal Al2O3. This work required the development of techniques to characterize the thermochemical stability of these fibers in different matrices.SEM/EDS elemental mapping was used for this work. To obtain qualitative compositional/spatial information, the best realistically achievable counting statistics were required. We established that 128 × 128 maps, acquired with a 20 KeV accelerating voltage, 3 sec. live time per pixel (total mapping time, 18 h) and with beam current adjusted to give 30% dead time, provided adequate image quality at a magnification of 800X. The maps were acquired, with backgrounds subtracted, using a Noran TN 5500 EDS system. The images and maps were transferred to a Macintosh and converted into TIFF files using either TIFF Maker, or TNtolMAGE, a Microsoft QuickBASIC program developed at the Science Center. From TIFF files, images and maps were opened in either NIH Image or Adobe Photoshop for processing and analysis and printed from Microsoft Powerpoint on a Kodak XL7700 dye transfer image printer.

Characterisation of multilayer materials using a position-sensitive atom probe

1990 ◽  
Vol 48 (4) ◽  
pp. 624-625
Author(s):  
RAD Mackenzie ◽  
G D W Smith ◽  
A. Cerezo ◽  
J A Liddle ◽  
CRM Grovenor ◽  
...  
Keyword(s):  
Quantum Well ◽  
Quantum Wells ◽  
Spatial Information ◽  
Chemical Vapour ◽  
Atom Probe ◽  
Organic Chemical ◽  
Growth Stages ◽  
Multiple Quantum ◽  
Quartz Wool ◽  
Position Sensitive

The position sensitive atom probe (POSAP), described briefly elsewhere in these proceedings, permits both chemical and spatial information in three dimensions to be recorded from a small volume of material. This technique is particularly applicable to situations where there are fine scale variations in composition present in the material under investigation. We report the application of the POSAP to the characterisation of semiconductor multiple quantum wells and metallic multilayers.The application of devices prepared from quantum well materials depends on the ability to accurately control both the quantum well composition and the quality of the interfaces between the well and barrier layers. A series of metal organic chemical vapour deposition (MOCVD) grown GaInAs-InP quantum wells were examined after being prepared under three different growth conditions. These samples were observed using the POSAP in order to study both the composition of the wells and the interface morphology. The first set of wells examined were prepared in a conventional reactor to which a quartz wool baffle had been added to promote gas intermixing. The effect of this was to hold a volume of gas within the chamber between growth stages, leading to a structure where the wells had a composition of GalnAsP lattice matched to the InP barriers, and where the interfaces were very indistinct. A POSAP image showing a well in this sample is shown in figure 1. The second set of wells were grown in the same reactor but with the quartz wool baffle removed. This set of wells were much better defined, as can be seen in figure 2, and the wells were much closer to the intended composition, but still with measurable levels of phosphorus. The final set of wells examined were prepared in a reactor where the design had the effect of minimizing the recirculating volume of gas. In this case there was again further improvement in the well quality. It also appears that the left hand side of the well in figure 2 is more abrupt than the right hand side, indicating that the switchover at this interface from barrier to well growth is more abrupt than the switchover at the other interface.

Phonological and Spatial Processing Abilities in Language- and Reading-Impaired Children

1988 ◽  
Vol 53 (3) ◽  
pp. 316-327 ◽  
Author(s):  
Alan G. Kamhi ◽  
Hugh W. Catts ◽  
Daria Mauer ◽  
Kenn Apel ◽  
Betholyn F. Gentry
Keyword(s):  
Phonological Processing ◽  
Spatial Information ◽  
Normal Children ◽  
Language Impaired ◽  
Word Repetition ◽  
Paper Folding ◽  
Syllable Segmentation ◽  
Processing Abilities ◽  
Impaired Children ◽  
Better Than

In the present study, we further examined (see Kamhi & Catts, 1986) the phonological processing abilities of language-impaired (LI) and reading-impaired (RI) children. We also evaluated these children's ability to process spatial information. Subjects were 10 LI, 10 RI, and 10 normal children between the ages of 6:8 and 8:10 years. Each subject was administered eight tasks: four word repetition tasks (monosyllabic, monosyllabic presented in noise, three-item, and multisyllabic), rapid naming, syllable segmentation, paper folding, and form completion. The normal children performed significantly better than both the LI and RI children on all but two tasks: syllable segmentation and repeating words presented in noise. The LI and RI children performed comparably on every task with the exception of the multisyllabic word repetition task. These findings were consistent with those from our previous study (Kamhi & Catts, 1986). The similarities and differences between LI and RI children are discussed.

Human Event-Related Potentials to Higher-Order Acoustic Spatial Changes

2002 ◽  
Vol 16 (2) ◽  
pp. 114-118 ◽  
Author(s):  
Timo Ruusuvirta ◽  
Heikki Hämäläinen
Keyword(s):  
Working Memory ◽  
Mismatch Negativity ◽  
Spatial Information ◽  
Free Field ◽  
Event Related Potentials ◽  
Negative Polarity ◽  
Positive Polarity ◽  
Spatial Changes ◽  
Related Potentials ◽  
Human Event

Abstract Human event-related potentials (ERPs) to a tone continuously alternating between its two spatial loci of origin (middle-standards, left-standards), to repetitions of left-standards (oddball-deviants), and to the tones originally representing these repetitions presented alone (alone-deviants) were recorded in free-field conditions. During the recordings (Fz, Cz, Pz, M1, and M2 referenced to nose), the subjects watched a silent movie. Oddball-deviants elicited a spatially diffuse two-peaked deflection of positive polarity. It differed from a deflection elicited by left-standards and commenced earlier than a prominent deflection of negative polarity (N1) elicited by alone-deviants. The results are discussed in the context of the mismatch negativity (MMN) and previous findings of dissociation between spatial and non-spatial information in auditory working memory.

Sign in / Sign up

Export Citation Format

Share Document