Hi! My name is Mara and I studied Molecular Biology and Biotechnology at TU Dresden. During my studies, I learned more about animals, plants and microbes and how they work than about computers. But in the context of the module "Applied Bioinformatics", I had a very engaging lecture about Bio-image Analysis held by Dr. Robert Haase. This gave the impulse for me to dive deeper into computer science and image analysis. In 2022, I became part of the Bio-image Analysis Group of Dr. Robert Haase at Physics of Life (PoL) in Dresden. First as a student assistant, now as a research assistant. My aim is to increase my knowledge about image analysis in python. I am excited about this interdisciplinary work and would like to facilitate and increase the exchange between computer scientists and biologists.
Scientific field: Biotechnology
Microscopy background: Image Analysis
Posted by Mara Lampert, on 1 June 2023In 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.
Posted by Mara Lampert, on 3 May 2023This 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,
Posted by Mara Lampert, on 13 April 2023This 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,
Posted by Mara Lampert, on 30 March 2023This 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
Posted by Mara Lampert, on 2 March 2023This 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