CellVision - Automatic segmentation of overlapping objects for cell image analysis

CellVision

In industrial and biomedical computer vision applications it is very important to deal with digital images which contain a large amount of overlapping objects. This leads to very useful applications such as cell imaging in the healthcare for diagnosis of cancer and nanoparticle imaging in the industry for quality control and material research. Our goal is to study automatic segmentation of overlapping objects. Manual segmentation is laborious, slow, and sensitive to interpretations. Images may contain tens of thousands of objects and it is time-consuming to detect attached and overlapping objects accurately. Recent developments in machine learning, especially with deep neural networks have enabled massive computations with large datasets.

This project continues the work that was done in the COMPHI project where the state-of-the-art methods for nanoparticle segmentation were developed for industrial purposes. The main aim of this project is to extend our approach to cell imaging for the modern digital healthcare.

The project includes international collaboration with the Laboratory for Image and Video Engineering (LIVE) at The University of Texas at Austin (UT) led by Professor Alan C. Bovik.

People

Sahar Zafari	visiting UT		Post-Doctoral Researcher
Tuomas Eerola	Office: 2422	Tel: +358 40 139 3405	Post-Doctoral Researcher, Project Manager
Jouni Sampo	Office: 2508	Tel: +358 44 337 5672	University Lecturer
Heikki Kälviäinen	Office: 2415	Tel: +358 40 586 7552	Professor, Project Leader

Publications

Resolving Overlapping Convex Objects in Silhouette Images by Concavity Analysis and Gaussian Process

By Sahar Zafari, Mariia Murashkina, Tuomas Eerola, Jouni Sampo, Heikki Kälviäinen, and Heikki Haario, In Journal of Visual Communication and Image Representation 73, 102962, 2020.

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Automated Segmentation of the Pectoral Muscle in Axial Breast MR Images

By Sahar Zafari, Mazen Diab, Tuomas Eerola, Summer Hanson, Greg Reece, Gary Whitman, Mia Markey, Krishnaswamy Ravi-Chandar, Alan Bovik, and Heikki Kälviäinen, In International Symposium on Visual Computing (ISVC 2019), 2019.

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Automated Segmentation of Nanoparticles in BF TEM Images by U-Net Binarization and Branch and Bound

By Sahar Zafari, Tuomas Eerola, Paulo Ferreira, Heikki Kälviäinen, and Alan Bovik, In 18th International Conference on Computer Analysis of Images and Patterns (CAIP 2019), 2019.

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Segmentation of Partially Overlapping Convex Objects in Silhouette Images

By Sahar Zafari, Doctoral dissertation, Lappeenranta-Lahti University of Technology LUT, 2018.

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CellVision: Automatic segmentation of overlapping objects for cell image analysis (Poster)

Sahar Zafari, Tuomas Eerola, Jouni Sampo, Heikki Kälviäinen, Heikki Haario, and Alan Bovik, In Opening seminar: Novel Applications of Artificial Intelligence in Physical Sciences and Engineering Research (AIPSE) 2018.

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Contour segment grouping for overlapping convex object segmentation

By Nikita Ashikhmin, Master's Thesis, Lappeenranta University of Technology, 2018.

Thesis presents a method that given a set of edge segments groups them according to the objects they belong to based on an assumption that the objects have a complex shape.