TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines

D Ershov, MS Phan, JW Pylvänäinen, SU Rigaud… - Nature …, 2022 - nature.com
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 …

A single-cell atlas of the normal and malformed human brain vasculature

EA Winkler, CN Kim, JM Ross, JH Garcia, E Gil, I Oh… - Science, 2022 - science.org
Cerebrovascular diseases are a leading cause of death and neurologic disability. Further
understanding of disease mechanisms and therapeutic strategies requires a deeper …

Recent advances in microfluidics-based cell migration research

J Ren, N Wang, P Guo, Y Fan, F Lin, J Wu - Lab on a Chip, 2022 - pubs.rsc.org
Cell migration is crucial for many biological processes, including normal development,
immune response, and tissue homeostasis and many pathological processes such as …

Democratising deep learning for microscopy with ZeroCostDL4Mic

L von Chamier, RF Laine, J Jukkala, C Spahn… - Nature …, 2021 - nature.com
Deep Learning (DL) methods are powerful analytical tools for microscopy and can
outperform conventional image processing pipelines. Despite the enthusiasm and …

[HTML][HTML] Disease-associated oligodendrocyte responses across neurodegenerative diseases

S Pandey, K Shen, SH Lee, YAA Shen, Y Wang… - Cell reports, 2022 - cell.com
Oligodendrocyte dysfunction has been implicated in the pathogenesis of neurodegenerative
diseases, so understanding oligodendrocyte activation states would shed light on disease …

An atlas of cortical arealization identifies dynamic molecular signatures

A Bhaduri, C Sandoval-Espinosa, M Otero-Garcia, I Oh… - Nature, 2021 - nature.com
The human brain is subdivided into distinct anatomical structures, including the neocortex,
which in turn encompasses dozens of distinct specialized cortical areas. Early …

An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer

KH Gouin III, N Ing, JT Plummer, CJ Rosser… - Nature …, 2021 - nature.com
Neoadjuvant chemotherapy (NAC) prior to surgery and immune checkpoint therapy (ICT)
have revolutionized bladder cancer management. However, stratification of patients that …

From pixels to insights: Machine learning and deep learning for bioimage analysis

M Jan, A Spangaro, M Lenartowicz… - BioEssays, 2024 - Wiley Online Library
Bioimage analysis plays a critical role in extracting information from biological images,
enabling deeper insights into cellular structures and processes. The integration of machine …

Automated deep lineage tree analysis using a Bayesian single cell tracking approach

K Ulicna, G Vallardi, G Charras… - Frontiers in Computer …, 2021 - frontiersin.org
Single-cell methods are beginning to reveal the intrinsic heterogeneity in cell populations,
arising from the interplay of deterministic and stochastic processes. However, it remains …

An adaptive stress response that confers cellular resilience to decreased ubiquitination

LC Hunt, V Pagala, A Stephan, B Xie, K Kodali… - Nature …, 2023 - nature.com
Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which
transfers ubiquitin to~ 35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it …