scholarly journals Probabilistic unsupervised classification for large-scale analysis of spectral imaging data

2022 ◽  
Vol 107 ◽  
pp. 102675
Author(s):  
Emmanuel Paradis
Keyword(s):  
Large Scale ◽  
Spectral Imaging ◽  
Unsupervised Classification ◽  
Scale Analysis ◽  
Imaging Data ◽  
Large Scale Analysis

scholarly journals Large-scale analysis, management, and retrieval of biological and medical images

2016 ◽  
Author(s):  
◽  
Jing Han
Keyword(s):  
Image Analysis ◽  
Big Data ◽  
Large Scale ◽  
Digital Pathology ◽  
Database Management System ◽  
Image Feature ◽  
Scale Analysis ◽  
Imaging Data ◽  
Data Infrastructure ◽  
Large Scale Analysis

Biomedical image data have been growing quickly in volume, speed, and complexity, and there is an increasing reliance on the analysis of these data. Biomedical scientists are in need of efficient and accurate analyses of large-scale imaging data, as well as innovative retrieval methods for visually similar imagery across a large-scale data collection to assist complex study in biological and medical applications. Moreover, biomedical images rely on increased resolution to capture subtle phenotypes of diseases, but this poses a challenge for clinicians to sift through haystacks of visual cues to make informative diagnoses. To tackle these challenges, we developed computational methods for large-scale analysis of biological and medical imaging data using simulated annealing to improve the quality of image feature extraction. Furthermore, we designed a Big Data infrastructure for the large-scale image analysis and retrieval of digital pathology images and conducted a longitudinal study of clinician's usage patterns of an image database management system (MDID) to shed light on the potential adoption of new informatics tools. This research also resulted in image analysis, management, and retrieval applications relevant to dermatology, radiology, pathology, life sciences, and palynology disciplines. These tools provide the potential to answer research questions that would not be answerable without our novel innovations that take advantage of Big Data technologies.

scholarly journals CellProfiler 4: improvements in speed, utility and usability

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
David R. Stirling ◽  
Madison J. Swain-Bowden ◽  
Alice M. Lucas ◽  
Anne E. Carpenter ◽  
Beth A. Cimini ◽  
...  
Keyword(s):  
Large Scale ◽  
Biological Information ◽  
Source Image ◽  
Scale Analysis ◽  
Imaging Data ◽  
Computational Tools ◽  
Large Scale Analysis ◽  
Improved Performance ◽  
Free Open Source ◽  
Microscopy Images

Abstract Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. 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. Results Herein we describe CellProfiler 4, a new version of this software with expanded functionality. 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 optimizations to reduce the time and cost associated with running common large-scale analysis pipelines. Conclusions CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years.

scholarly journals Identifying draught cattle in the past: Lessons from large-scale analysis of archaeological datasets

2021 ◽  
Vol 33 ◽  
pp. 258-269
Author(s):  
Matilda Holmes ◽  
Richard Thomas ◽  
Helena Hamerow
Keyword(s):  
Large Scale ◽  
Scale Analysis ◽  
The Past ◽  
Large Scale Analysis

scholarly journals Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

2021 ◽  
Author(s):  
Mehdi A. Beniddir ◽  
Kyo Bin Kang ◽  
Grégory Genta-Jouve ◽  
Florian Huber ◽  
Simon Rogers ◽  
...  
Keyword(s):  
Natural Product ◽  
Large Scale ◽  
Scale Analysis ◽  
Computational Tools ◽  
Natural Product Discovery ◽  
Large Scale Analysis ◽  
Metabolite Annotation

This review highlights the key computational tools and emerging strategies for metabolite annotation, and discusses how these advances will enable integrated large-scale analysis to accelerate natural product discovery.

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