Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.

ABSTRACT:

Summary

We introduce YeastSpotter, a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.

Availability and implementation

YeastSpotter is available at http://yeastspotter.csb.utoronto.ca/. Code is available at https://github.com/alexxijielu/yeast_segmentation.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Lu AX

PROVIDER: S-EPMC6821424 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.

Lu Alex X AX Zarin Taraneh T Hsu Ian S IS Moses Alan M AM

Bioinformatics (Oxford, England) 20191101 21

<h4>Summary</h4>We introduce YeastSpotter, a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.<h4>Availability and implementation</h4>YeastSpotter is available at http://yeastspotter.csb.utoronto.ca/. Code is available at https://github.com/alexxijielu/yeast_segmentation.<h4>Supplementary information ...[more]

PMID: 31095270

Similar Datasets

Parameter-free rendering of single-molecule localization microscopy data for parameter-free resolution estimation.

Project description:Localization microscopy is a super-resolution imaging technique that relies on the spatial and temporal separation of blinking fluorescent emitters. These blinking events can be individually localized with a precision significantly smaller than the classical diffraction limit. This sub-diffraction localization precision is theoretically bounded by the number of photons emitted per molecule and by the sensor noise. These parameters can be estimated from the raw images. Alternatively, the resolution can be estimated from a rendered image of the localizations. Here, we show how the rendering of localization datasets can influence the resolution estimation based on decorrelation analysis. We demonstrate that a modified histogram rendering, termed bilinear histogram, circumvents the biases introduced by Gaussian or standard histogram rendering. We propose a parameter-free processing pipeline and show that the resolution estimation becomes a function of the localization density and the localization precision, on both simulated and state-of-the-art experimental datasets.

| S-EPMC8113488 | biostudies-literature

A Robust Parameter-free Thresholding Method for Image Segmentation.

Project description:In this work we presented a new parameter-free thresholding method for image segmentation. In separating an image into two classes, the method employs an objective function that not only maximizes the between-class variance but also the distance between the mean of each class and the global mean of the image. The design of the objective function aims to circumvent the challenge that many existing techniques encounter when the underlying two classes have very different sizes or variances. Advantages of the new method are two-fold. First, it is parameter-free, meaning that it can generate consistent results. Second, the new method has a simple form that makes it easy to adapt to different applications. We tested and compared the new method with the standard Otsu method, the maximum entropy method, and the 2D Otsu method on simulated and real biomedical and photographic images and found the new method can achieve a more accurate and robust performance.

| S-EPMC6640864 | biostudies-literature

Self-supervised semantic segmentation of retinal pigment epithelium cells in flatmount fluorescent microscopy images.

Project description:MotivationMorphological analyses with flatmount fluorescent images are essential to retinal pigment epithelial (RPE) aging studies and thus require accurate RPE cell segmentation. Although rapid technology advances in deep learning semantic segmentation have achieved great success in many biomedical research, the performance of these supervised learning methods for RPE cell segmentation is still limited by inadequate training data with high-quality annotations.ResultsTo address this problem, we develop a Self-Supervised Semantic Segmentation (S4) method that utilizes a self-supervised learning strategy to train a semantic segmentation network with an encoder-decoder architecture. We employ a reconstruction and a pairwise representation loss to make the encoder extract structural information, while we create a morphology loss to produce the segmentation map. In addition, we develop a novel image augmentation algorithm (AugCut) to produce multiple views for self-supervised learning and enhance the network training performance. To validate the efficacy of our method, we applied our developed S4 method for RPE cell segmentation to a large set of flatmount fluorescent microscopy images, we compare our developed method for RPE cell segmentation with other state-of-the-art deep learning approaches. Compared with other state-of-the-art deep learning approaches, our method demonstrates better performance in both qualitative and quantitative evaluations, suggesting its promising potential to support large-scale cell morphological analyses in RPE aging investigations.Availability and implementationThe codes and the documentation are available at: https://github.com/jkonglab/S4_RPE.

| S-EPMC10139776 | biostudies-literature

Benchmark for multi-cellular segmentation of bright field microscopy images.

Project description:BackgroundMulti-cellular segmentation of bright field microscopy images is an essential computational step when quantifying collective migration of cells in vitro. Despite the availability of various tools and algorithms, no publicly available benchmark has been proposed for evaluation and comparison between the different alternatives.DescriptionA uniform framework is presented to benchmark algorithms for multi-cellular segmentation in bright field microscopy images. A freely available set of 171 manually segmented images from diverse origins was partitioned into 8 datasets and evaluated on three leading designated tools.ConclusionsThe presented benchmark resource for evaluating segmentation algorithms of bright field images is the first public annotated dataset for this purpose. This annotated dataset of diverse examples allows fair evaluations and comparisons of future segmentation methods. Scientists are encouraged to assess new algorithms on this benchmark, and to contribute additional annotated datasets.

| S-EPMC3826518 | biostudies-literature

Intelligent contour extraction approach for accurate segmentation of medical ultrasound images.

Project description:Introduction: Accurate contour extraction in ultrasound images is of great interest for image-guided organ interventions and disease diagnosis. Nevertheless, it remains a problematic issue owing to the missing or ambiguous outline between organs (i.e., prostate and kidney) and surrounding tissues, the appearance of shadow artifacts, and the large variability in the shape of organs. Methods: To address these issues, we devised a method that includes four stages. In the first stage, the data sequence is acquired using an improved adaptive selection principal curve method, in which a limited number of radiologist defined data points are adopted as the prior. The second stage then uses an enhanced quantum evolution network to help acquire the optimal neural network. The third stage involves increasing the precision of the experimental outcomes after training the neural network, while using the data sequence as the input. In the final stage, the contour is smoothed using an explicable mathematical formula explained by the model parameters of the neural network. Results: Our experiments showed that our approach outperformed other current methods, including hybrid and Transformer-based deep-learning methods, achieving an average Dice similarity coefficient, Jaccard similarity coefficient, and accuracy of 95.7 ± 2.4%, 94.6 ± 2.6%, and 95.3 ± 2.6%, respectively. Discussion: This work develops an intelligent contour extraction approach on ultrasound images. Our approach obtained more satisfactory outcome compared with recent state-of-the-art approaches . The knowledge of precise boundaries of the organ is significant for the conservation of risk structures. Our developed approach has the potential to enhance disease diagnosis and therapeutic outcomes.

| S-EPMC10479019 | biostudies-literature

Accurate determination of marker location within whole-brain microscopy images.

Project description:High-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and labelled cell populations that are necessary to interpret in vivo experiments designed to understand brain function. Here we have developed two plugins (brainreg and brainreg-segment) for the Python-based image viewer napari, to accurately map any object in a common coordinate space. We analysed the position of dye-labelled electrode tracks and two-photon imaged cell populations expressing fluorescent proteins. The precise location of probes and cells were physiologically interrogated and revealed accurate segmentation with near-cellular resolution.

| S-EPMC8766598 | biostudies-literature

Weighted average ensemble-based semantic segmentation in biological electron microscopy images.

Project description:Semantic segmentation of electron microscopy images using deep learning methods is a valuable tool for the detailed analysis of organelles and cell structures. However, these methods require a large amount of labeled ground truth data that is often unavailable. To address this limitation, we present a weighted average ensemble model that can automatically segment biological structures in electron microscopy images when trained with only a small dataset. Thus, we exploit the fact that a combination of diverse base-learners is able to outperform one single segmentation model. Our experiments with seven different biological electron microscopy datasets demonstrate quantitative and qualitative improvements. We show that the Grad-CAM method can be used to interpret and verify the prediction of our model. Compared with a standard U-Net, the performance of our method is superior for all tested datasets. Furthermore, our model leverages a limited number of labeled training data to segment the electron microscopy images and therefore has a high potential for automated biological applications.

| S-EPMC9630254 | biostudies-literature

Accurate model-based segmentation of gynecologic brachytherapy catheter collections in MRI-images.

Project description:The gynecological cancer mortality rate, including cervical, ovarian, vaginal and vulvar cancers, is more than 20,000 annually in the US alone. In many countries, including the US, external-beam radiotherapy followed by high dose rate brachytherapy is the standard-of-care. The superior ability of MR to visualize soft tissue has led to an increase in its usage in planning and delivering brachytherapy treatment. A technical challenge associated with the use of MRI imaging for brachytherapy, in contrast to that of CT imaging, is the visualization of catheters that are used to place radiation sources into cancerous tissue. We describe here a precise, accurate method for achieving catheter segmentation and visualization. The algorithm, with the assistance of manually provided tip locations, performs segmentation using image-features, and is guided by a catheter-specific, estimated mechanical model. A final quality control step removes outliers or conflicting catheter trajectories. The mean Hausdorff error on a 54 patient, 760 catheter reference database was 1.49? mm; 51 of the outliers deviated more than two catheter widths (3.4? mm) from the gold standard, corresponding to catheter identification accuracy of 93% in a Syed-Neblett template. In a multi-user simulation experiment for evaluating RMS precision by simulating varying manually-provided superior tip positions, 3? maximum errors were 2.44? mm. The average segmentation time for a single catheter was 3?s on a standard PC. The segmentation time, accuracy and precision, are promising indicators of the value of this method for clinical translation of MR-guidance in gynecologic brachytherapy and other catheter-based interventional procedures.

| S-EPMC5654713 | biostudies-other

Segmentation and intensity estimation for microarray images with saturated pixels

Project description:Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels

2011-11-23 | GSE33899 | GEO

Segmentation and intensity estimation for microarray images with saturated pixels

Project description:Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels Three immunosignatures from human Valley Fever (Coccidiodes) patients and three immunosignatures from human influenza vaccine recipients were examined to test an algorithm that extends the apparent dynamic range of a fluorescence image. These images had several saturated spots at 70PMT and 100% laser power. The program examined the differences between Valley Fever and influenza in terms of standard image processing vs. segmentation and intensity estimation.

2011-11-23 | E-GEOD-33899 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data