25 papers · ranked by Valyu relevance
Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen + 1 more
'Eija Jokitalo'] Understanding the structure-function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the…
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen + 23 more
'Jeremy L. Muhlich' 'Joshua Hess' 'Allison L. Creason' 'Ajit J. Nirmal' 'Gregory J. Baker' 'Maulik K. Nariya' 'Jia-Ren Lin' 'Zoltan Maliga' 'Connor A. Jacobson' 'Matthew W. Hodgman' 'Juha Ruokonen' 'Samouil L. Farhi' 'Domenic Abbondanza' 'Eliot T. McKinley' 'Daniel Persson' 'Courtney Betts' 'Shamilene Sivagnanam' 'Aviv…
Lena R. Bartell, Lawrence J. Bonassar, Itai Cohen
Imaging assays of cellular function, especially those using fluorescent stains, are ubiquitous in the biological and medical sciences. Despite advances in computer vision, such images are often analyzed using only manual or rudimentary automated processes. Watershed-based segmentation is an effective technique for…
Peter Bajcsy, Antonio Cardone, Joe Chalfoun, Michael Halter + 8 more
Background The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are denoted as two- or three-dimensional (2D or 3D) image…
Matthias Arzt, Joran Deschamps, Christopher Schmied, Tobias Pietzsch + 3 more
We present Labkit, a user-friendly Fiji plugin for the segmentation of microscopy image data. It offers easy to use manual and automated image segmentation routines that can be rapidly applied to single- and multi-channel images as well as to timelapse movies in 2D or 3D. Labkit is specifically designed to work…
Soonam Lee, Chichen Fu, Paul Salama, Kenneth W. Dunn + 1 more
'Edward J. Delp'] Fluorescence microscopy has become a widely used tool for studying various biological structures of in vivo tissue or cells. However, quantitative analysis of these biological structures remains a challenge due to their complexity which is exacerbated by distortions caused by lens aberrations and…
Noah Dolev, Lior Pinkus, Michal Rivlin-Etzion
The availability of genetically modified calcium indicators has made calcium imaging of neural signaling accessible and widespread whereby recording hundreds or even thousands of cells simultaneously is commonplace. Immunocytochemistry also produces large images with a great number of antibody labeled cells. A major…
Laura Wiggins, Peter J. O’Toole, William J. Brackenbury, Julie Wilson
Segmentation and tracking are essential preliminary steps in the analysis of almost all live cell imaging applications. Although the number of open-source software systems that facilitate automated segmentation and tracking continue to evolve, many researchers continue to opt for manual alternatives for samples that…
Anuradha Kar, Manuel Petit, Yassin Refahi, Guillaume Cerutt + 2 more
Segmenting three dimensional microscopy images is essential for understanding phenomena like morphogenesis, cell division, cellular growth and genetic expression patterns. Recently, deep learning (DL) pipelines have been developed which claim to provide high accuracy segmentation of cellular images and are increasingly…
Bálint Antal, Bence Remenyik, András Hajdú
In this paper, we propose an approach to the unsupervised segmentation of images using Markov Random Field. The proposed approach is based on the idea of Bit Plane Slicing. We use the planes as initial labellings for an ensemble of segmentations. With pixelwise voting, a robust segmentation approach can be achieved…
Lin Zhang
Phase contrast microscopy (PCM) has been widely used in the biomedicine, which allows users to observe objectives without staining or killing them. One important related research is to employ PCM to monitor live cells. How to segment cell populations in obtained PCM images gains more and more attention as its a…
E. Josiah Lutton, Sharon Collier, Till Bretschneider
High-resolution 3D microscopy is a fast advancing field and requires new techniques in image analysis to handle these new datasets. In this work, we focus on detailed 3D segmentation of Dictyostelium cells undergoing macropinocytosis captured on an iSPIM microscope. We propose a novel random walker-based method with a…
Elco Bakker, Peter S. Swain, Matthew M. Crane
Although high-content image cytometry is becoming increasingly routine, processing the large amount of data acquired during time-lapse experiments remains a challenge. The majority of approaches for automated single-cell segmentation focus on flat, uniform fields of view covered with a single layer of cells. In the…
Julia Sistermanns, Ellen Emken, Gregor Weirich, Oliver Hayden + 1 more
'Wolfgang Utschick'] Abstract—In the effort to aid cytologic diagnostics by establishing automatic single-cell screening using high-throughput digital holographic microscopy for clinical studies thousands of images and millions of cells are captured. The bottleneck lies in an automatic, fast, and unsupervised…
Richard J Giuly, Maryann E Martone, Mark H Ellisman
Background While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this…
Giuseppe Giacopelli, Michele Migliore, Domenico Tegolo
Background: Image analysis applications in digital pathology include various methods for segmenting regions of interest. Their identification is one of the most complex steps, and therefore of great interest for the study of robust methods that do not necessarily rely on a machine learning (ML) approach. Method: A…
Elaine ML Ho, Dimitrios Ladakis, Mark Basham, Michele C Darrow
Segmentation of biological images identifies regions of an image which correspond to specific features of interest, which can be analysed quantitatively to answer biological questions. This task has long been a barrier to conducting large-scale biological imaging studies as it is time- and labour-intensive. Modern…
Juliana M Haggerty, Xiao N Wang, Anne Dickinson, Chris J O’Malley + 1 more
'Elaine B Martin'] Background Digital image analysis has the potential to address issues surrounding traditional histological techniques including a lack of objectivity and high variability, through the application of quantitative analysis. A key initial step in image analysis is the identification of regions of…
Anubha Gupta, Pramit Mallick, Ojaswa Sharma, Ritu Gupta + 2 more
'Rahul Duggal' 'Yuanquan Wang'] Plasma cell segmentation is the first stage of a computer assisted automated diagnostic tool for multiple myeloma (MM). Owing to large variability in biological cell types, a method for one cell type cannot be applied directly on the other cell types. In this paper, we present PCSeg Tool…
Pedro Nogueira
Firstly, I would like to thank my advisor, Prof. Miguel Coimbra, for all the opportunities and challenges he provided, for the continued support, for his patience, enthusiasm, availability and last but not least, for inciting me to push ever further and grow. In sum, I'd like to offer my most honest gratitude for…
Mohammed M. Abdelsamea
In this paper, an automatic seeded region growing algorithm is proposed for cellular image segmentation. First, the regions of interest (ROIs) extracted from the preprocessed image. Second, the initial seeds are automatically selected based on ROIs extracted from the image. Third, the most reprehensive seeds are…
Alexander E. Siemenn, Eunice Aissi, Fang Sheng, Armi Tiihonen + 3 more
In materials research, the task of characterizing hundreds of different materials traditionally requires equally many human hours spent measuring samples one by one. We demonstrate that with the integration of computer vision into this material research workflow, many of these tasks can be automated, significantly…
Authors not listed
During charge/discharge cracking occurs in Nickel Manganese Cobalt (NMC) secondary particles. Secondary particles with cracks will have observably lower grey-levels in micro-CT datasets compared to an otherwise identical pristine particle. This is due to the ‘partial volume effect’ where voxels representative of space…
Abbas Jabermoradi, John van Duynhoven, Johannes Hohlbein
Emulsifiers play an essential role in ensuring the physiochemical stability of food emulsions. In the case of mayonnaise, proteins contained in egg yolk act as emulsifiers. Here, we employed stochastic optical reconstruction microscopy (STORM) to localize proteins at the oil/water droplet interface using fluorescently…
Kanda Borgognoni, Bradley Guilliams, Rachel Cohen, Christopher Ackerson
A cloneable NanoParticle (cNP) is an inorganic nanoparticle that is synthesized by a protein. The protein determines the elemental composition, size, morphology, and other properties of the nanoparticle. Here, we describe the use of a cloneable Selenium NanoParticle (cSeNP) as a cloneable imaging contrast agent in…