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Advancing human induced pluripotent stem cell derived cardiomyocyte (hiPSC-CM) technology will lead to significant progress ranging from disease modeling, to drug discovery, to regenerative tissue engineering. Yet, alongside these potential…
Brightfield time-lapse imaging is widely used in cardiac tissue engineering, yet the absence of standardized, interpretable analytical frameworks limits reproducibility and cross-platform comparison. We present an open, scalable…
Timelapse images of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide rich information on cell structure and contractile function. However, it is challenging to reproducibly generate tissue samples and conduct…
Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical…
Medical image processing demands specialized software that handles high-dimensional volumetric data, heterogeneous file formats, and domain-specific training procedures. Existing frameworks either provide low-level components that require…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
Background: In vitro endothelial cell culture is widely used to study angiogenesis. Histomicrographic images of cell networks are often analyzed manually, a process that is time-consuming and subjective. Automated tools like ImageJ (NIH)…
Understanding the architecture of the human heart requires analysis of its microstructural organization across scales. With the advent of high-resolution imaging techniques such as synchrotron-based tomography, it has become possible to…
The contractile motion of the heart is strongly determined by the distribution of the fibers that constitute cardiac tissue. Strain analysis informed with the orientation of fibers allows to describe several pathologies that are typically…
Anatomic tracer studies are critical for validating and improving diffusion MRI (dMRI) tractography. However, large-scale analysis of data from such studies is hampered by the labor-intensive process of annotating fiber bundles manually on…
Parcellation of whole-brain tractography streamlines is an important step for tract-based analysis of brain white matter microstructure. Existing fiber parcellation approaches rely on accurate registration between an atlas and the…
Photoplethysmography is a non-invasive optical technique that measures changes in blood volume within tissues. It is commonly and increasingly used for in a variety of research and clinical application to assess vascular dynamics and…
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are an effective tool for studying cardiac function and disease, and hold promise for screening drug effects on human tissue. Changes to motion patterns in these cells…
Fast, incremental evolution of physics instrumentation raises the question of efficient software abstraction and transferability of algorithms across similar technologies. This contribution aims to provide an answer by introducing Track…
We introduce cellanneal, a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimization of Spearman's rank correlation coefficient between experimental and computational mixture gene expression…
We introduce pymovements: a Python package for analyzing eye-tracking data that follows best practices in software development, including rigorous testing and adherence to coding standards. The package provides functionality for key…
Developing foundation models in medical imaging requires continuous monitoring of downstream performance. Researchers are burdened with tracking numerous experiments, design choices, and their effects on performance, often relying on…
Spectropolarimetry, the observation of polarization and intensity as a function of wavelength, is a powerful tool in stellar astrophysics. It is particularly useful for characterizing stars and circumstellar material, and for tracing the…
PyUnfold is a Python package for incorporating imperfections of the measurement process into a data analysis pipeline. In an ideal world, we would have access to the perfect detector: an apparatus that makes no error in measuring a desired…
mmid (Multi-Modal Integration and Downstream analyses for healthcare analytics) is a Python package that offers multi-modal fusion and imputation, classification, time-to-event prediction and clustering functionalities under a single…