The Fiji platform, a cornerstone in scientific imaging, has undergone several major developments to meet evolving community needs, focusing on cross-language integration and modernization to enhance its utility and accessibility.
Recent key initiatives include: upgrading Fiji to OpenJDK 21 with the new Jaunch launcher, which supports both JVM and Python runtimes; developing SciJava Ops for...
Measuring the quality of fluorescence microscopy images is critical for applications including automated image acquisition and image processing. Most image quality metrics used are full-reference metrics, where a test image is quantitatively compared to a reference or ‘ground truth’ image. Commonly used full-reference metrics in fluorescence microscopy include NRMSE, PSNR, SSIM and Pearson’s...
Machine learning (ML) is becoming pivotal in life science research, offering powerful tools for interpreting complex biological data. In particular, explainable ML provides insights into the reasoning behind model predictions, highlighting the data features that drove the model outcome. Our work focuses on building explainable ML models for microscopy images. These models not only classify...
Cell mechanics impact cell shape and drive crucial morphological changes during development and disease. However, quantifying mechanical parameters in living cells in a tissue context is challenging. Here, we introduce OptiCell3D, a computational pipeline to infer mechanical properties of cells from 3D microscopy images. OptiCell3D leverages a deformable cell model and gradient-based...
