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Feature extraction in napari

Posted by , on 3 May 2023

This blog post revolves around extracting and selecting features from segmented images. We will define the terms feature extraction and selection. Also, we will learn how to categorize features and can look up specific features in a glossary. Furthermore, we will explore how to extract features in napari. Definition of feature extraction During feature extraction,
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Quality assurance of segmentation results

Posted by , on 13 April 2023

This blog post revolves around determining and improving the quality of segmentation results. A common problem is that this step is often omitted and done rather by the appearance of the image segmentation than by actually quantifying it. This blogpost aims to show different ways to achieve this quantification as this leads to reproducibility. Therefore,
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Annotating 3D images in napari

Posted by , on 30 March 2023

This blog post revolves around generating ground truth in 3D images for segmentation. Therefore, we will define what ground truth is and how we can generate it using napari in a time-efficient way. We will also learn about difficulties of annotating alone or in groups and address possible solutions for both. Challenges of image segmentation
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Fast4DReg - to the rescue of your drifty microscopy data

Posted by , on 10 March 2023

Fast4DReg to the rescue of your 4D microscopy data In life sciences, researchers use microscopes to study living organisms, such as cells or small animals. These live cell imaging experiments are usually performed over several hours, exposing the experiment to changes in the sample and in the microscope surroundings – causing the data to drift.
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Rescaling images and pixel (an)isotropy

Posted by , on 2 March 2023

This blog post shows the importance of rescaling 3D image data and what anisotropy of pixels/voxels has to do with it. We will see which different options exist to rescale an image as well as their advantages and limitations. We will also apply a commonly used segmentation algorithm, Voronoi-Otsu-Labeling, on the original and the rescaled
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Image Analyst at Harvard Medical School

Posted by , on 27 February 2023

We are looking for two or more smart, skilled, and enthusiastic bioimage analysts, to join us as soon as possible. Harvard Medical School (HMS) is a world leader in biological and biomedical imaging, with an outstanding community of researchers using cutting-edge microscopy to advance the field. The Image Analysis Collaboratory (IAC) is dedicated to training
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AI4Life First Open Call

Posted by , on 20 February 2023

The European project AI4Life aims at narrowing the gap between life scientists performing biological imaging and developers of AI-based methods to analyze microscopy image data.  This is the first of a series of annual open calls, meant to provide life scientists who have unmet image analysis needs with adequate deep learning enhanced workflows for their
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Job Opportunity: Scientific Officer on Smart Microscopy at the Centre for Cellular Imaging of Gothenburg University

Posted by , on 9 January 2023

We are looking for a new colleague (Scientific Officer) at the Centre for Cellular Imaging of Gothenburg University (CCI). The CCI, in operation since 2003, is a national research infrastructure and one of the leading academic imaging facilities in Sweden providing expertise and access to advanced microscopy to the research community, both locally and at other Swedish
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Crick BioImage Analysis Symposium (CBIAS) 2022 - a review

Posted by , on 14 December 2022

Did you want to participate in the Crick BioImage Analysis Symposium (CBIAS) but missed it? Are you planning to join us next year for CBIAS2023 but unsure if it would be relevant for you? We’ve asked three of this year’s participants to tell us about their experience and collated their reports here! We’ll hear from
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FocalPlane features... Quantitative Phase Imaging

Posted by , on 6 July 2022

In case you missed ‘FocalPlane features…’ last month, here is the recording of the webinar given by Zuzana Nováková, Patrick McCall and Jan Balvan on Thursday 30 June 2022.
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