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Displaying posts in the category: How to

Sharing Your Poster on Figshare: A Community Guide to How-To and Why

Posted by Elisabeth Kugler, on 26 July 2023

Join the Open Science revolution and increase the impact of your research by sharing it on Figshare. Discover the benefits of transparency, collaboration, and accessibility in science as you make your work citable, shareable, and discoverable. Our step-by-step guide will walk you through uploading your conference posters and data, ensuring your research reaches a wider

Tracking in napari

Posted by Mara Lampert, on 1 June 2023

In this blog post we are exploring cell tracking in napari. Two important processes in normal tissue development and disease are cell migration and proliferation. To gain a better understanding on these processes, tracking in time-lapse datasets is needed. By measuring track properties, like velocity and the total travelled distance, spatio-temporal relationships can be studied.

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,

Conference Tips from the yDGE

Posted by yDGE, on 26 April 2023

About yDGE DGE Young Microscopists, abbreviated yDGE, is a working group within the German Society for Electron Microscopy (DGE) for students, doctoral researchers, as well as early-career post-doctoral researchers and professionals. In January 2022, we started as a small (but all the more motivated) group of peers. Our vision was, and still is, to promote

Bypassing 164 years of tradition with 'any immersion microscopy'

Posted by Alfred Millett-Sikking, on 24 April 2023

The optical microscope is a classic scientific instrument with a straightforward purpose: to observe objects in more detail than is possible with the naked eye. Many microscope variations exist, from the rudimentary examples of the 17th century, to modern computer controlled systems with sophisticated designs. Despite the variety, most optical microscopes reuse the same physical

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

Sharing research data with Zenodo

Posted by Robert Haase, on 15 February 2023

TL;DR: Sharing data open access is good scientific practice. If data is shared via online portals such as https://zenodo.org, we can implement best practices for sharing, licensing, reusing and citing research data. In this blog post I guide through the minimal procedures that are necessary to share a dataset publicly following the FAIR principles; to

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Microscopy-related articles from our journals

HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples Development 2024 151: dev202307
filoVision – using deep learning and tip markers to automate filopodia analysis J Cell Sci 2024 137: jcs261274
C omputational tools for quantifying actin filament numbers, lengths, and bundling Biology Open 2024 13: bio.060267

Microscopy-related preprint highlights

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