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Microscopy preprints – bioimage analysis tools

Posted by FocalPlane, on 25 August 2023

Here is a curated selection of preprints published recently. In this post, we focus specifically on new tools for bioimage analysis.

Microscopy preprints – bioimage analysis tools

Posted by FocalPlane, on 14 July 2023

Here is a curated selection of preprints published recently. In this post, we focus specifically on new bioimage analysis tools, including a number of preprints on generative AI.

The Company of Biologists Workshops 2025

Posted by FocalPlane, on 12 June 2023

Do you have an idea for a new Workshop, but are not sure that you have time to take care of all the planning? You can apply to organise a Workshop with The Company of Biologists and while you take care of the science, our events team will organise the logistics of the meeting. We

Microscopy preprints – bioimage analysis tools

Posted by FocalPlane, on 6 June 2023

Here is a curated selection of preprints published recently. In this post, we focus specifically on preprints on bioimage analysis.

AI4Life at the 5th NEUBIAS Conference

Posted by Estibaliz Gómez-de-Mariscal, on 26 May 2023

AI4Life recently participated in the 5th NEUBIAS Conference in Porto, Portugal, a two-part event comprising the Defragmentation Training School and the Open Symposium. This conference brought together experts and enthusiasts in the field of BioImage Analysis (BIA) to explore cutting-edge techniques and advancements in the integration of cloud computing. Under the umbrella of AI4Life, there

Feature extraction in napari

Posted by Mara Lampert, 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,

Quality assurance of segmentation results

Posted by Mara Lampert, 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,

Annotating 3D images in napari

Posted by Mara Lampert, 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

Fast4DReg - to the rescue of your drifty microscopy data

Posted by Joanna Pylvänäinen, 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.

Rescaling images and pixel (an)isotropy

Posted by Mara Lampert, 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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Microscopy-related articles from our journals

Efficient and rapid fluorescent protein knock-in with universal donors in mouse embryonic stem cells Development 2023 150: dev201367
Direct fluorescent labeling of NF186 and NaV1.6 in living primary neurons using bioorthogonal click chemistry J Cell Sci 2023 136: jcs260600
An automated microscopy workflow to study Shigella–neutrophil interactions and antibiotic efficacy in vivo Disease Models & Mechanisms 2023 16: dmm049908

Microscopy-related preprint highlights

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Microscopy-related articles from our journals

Microscopy-related preprint highlights

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