Lecture

ABBA Workflow: Image Processing and Analysis

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Description

This lecture introduces the ABBA workflow, focusing on the integration of QuPath projects with images hosted on OMERO. The instructor demonstrates how to import a QuPath project, run the DeepSlice algorithm for image segmentation, and utilize Elastix for image registration. The process culminates in exporting the processed images back to the QuPath project. The lecture covers the necessary steps for aligning and analyzing brain images, specifically using the Adult Mouse Brain from the Allen Brain Atlas. The instructor emphasizes the importance of accurate image processing techniques in biological research, showcasing the tools available within the BIOP Desktop environment. The audience gains insights into the practical applications of these methods in neuroscience and histology, enhancing their understanding of image analysis workflows.

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Related concepts (32)

Image segmentation

In and computer vision, image segmentation is the process of partitioning a into multiple image segments, also known as image regions or image objects (sets of pixels). The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze. Image segmentation is typically used to locate objects and boundaries (lines, curves, etc.) in images. More precisely, image segmentation is the process of assigning a label to every pixel in an image such that pixels with the same label share certain characteristics.

Medical image computing

Medical image computing (MIC) is an interdisciplinary field at the intersection of computer science, information engineering, electrical engineering, physics, mathematics and medicine. This field develops computational and mathematical methods for solving problems pertaining to medical images and their use for biomedical research and clinical care. The main goal of MIC is to extract clinically relevant information or knowledge from medical images.

Image registration

Image registration is the process of transforming different sets of data into one coordinate system. Data may be multiple photographs, data from different sensors, times, depths, or viewpoints. It is used in computer vision, medical imaging, military automatic target recognition, and compiling and analyzing images and data from satellites. Registration is necessary in order to be able to compare or integrate the data obtained from these different measurements.

Data and information visualization

Data and information visualization (data viz or info viz) is the practice of designing and creating easy-to-communicate and easy-to-understand graphic or visual representations of a large amount of complex quantitative and qualitative data and information with the help of static, dynamic or interactive visual items.

Object co-segmentation

In computer vision, object co-segmentation is a special case of , which is defined as jointly segmenting semantically similar objects in multiple images or video frames. It is often challenging to extract segmentation masks of a target/object from a noisy collection of images or video frames, which involves object discovery coupled with . A noisy collection implies that the object/target is present sporadically in a set of images or the object/target disappears intermittently throughout the video of interest.

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