Joanna Pylvänäinen

Åbo Akademi University · Department of Biology

Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality and efficiency and can sign...

Leukocyte extravasation is a key component of the innate immune response, while circulating tumor cell extravasation is a critical step in metastasis formation. Despite their importance, the mechanisms underlying leukocyte and tumor cell extravasation remain incompletely understood. Here, we developed an imaging pipeline that integrates fast, label...

In life sciences, tracking objects from movies enables researchers to quantify the behavior of single particles, organelles, bacteria, cells, and even whole animals. While numerous tools now allow automated tracking from video, a significant challenge persists in compiling, analyzing, and exploring the large datasets generated by these approaches....

Fluorescence microscopy is essential for studying living cells, tissues and organisms. However, the fluorescent light that switches on fluorescent molecules also harms the samples, jeopardizing the validity of results – particularly in techniques such as super-resolution microscopy, which demands extended illumination. Artificial intelligence (AI)-...

Deep learning has revolutionised the analysis of extensive microscopy datasets, yet challenges persist in the widespread adoption of these techniques. Many lack access to training data, computing resources, and expertise to develop complex models. We introduce DL4MicEverywhere, advancing our previous ZeroCostDL4Mic platform, to make deep learning m...

Fluorescence microscopy, widely used in the study of living cells, tissues, and organisms, often faces the challenge of photodamage. This is primarily caused by the interaction between light and biochemical components during the imaging process, leading to compromised accuracy and reliability of biological results. Methods necessitating extended hi...

Unwanted sample drift is a common issue that plagues microscopy experiments, preventing accurate temporal visualization and quantification of biological processes. While multiple methods and tools exist to correct images post-acquisition, performing drift correction of 3D videos using open-source solutions remains challenging and time-consuming. He...

TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitativel...

TrackMate is an automated tracking software used to analyze bioimages and distributed as a Fiji plugin. Here we introduce a new version of TrackMate rewritten to improve performance and usability, and integrating several popular machine and deep learning algorithms to improve versatility. We illustrate how these new components can be used to effici...

For maximal oncogenic activity, cellular MYC protein levels need to be tightly controlled so that they do not induce apoptosis. Here, we show how ubiquitin ligase UBR5 functions as a molecular rheostat to prevent excess accumulation of MYC protein. UBR5 ubiquitinates MYC and its effects on MYC protein stability are independent of FBXW7. Silencing o...

MYC protein expression has to be tightly controlled to allow for maximal cell proliferation without inducing apoptosis. Here we discover UBR5 as a novel MYC ubiquitin ligase and demonstrate how it functions as a molecular rheostat to prevent excess accumulation of MYC protein. UBR5 effects on MYC protein stability are independent on N-terminal FBW7...

Nestin, an intermediate filament protein and marker of undifferentiated cells is expressed in several cancers. Nestin is important for neuronal survival and is a regulator of myogenesis but its function in malignancy is ambiguous. We show that nestin-downregulation led to a redistribution of pFAK to focal adhesions (FA) and alterations in FA turnov...