Related papers: CellProfiler plugins -- an easy image analysis pla…
Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free, open-source software package designed for the exploration…
Biological image analysis has traditionally focused on measuring specific visual properties of interest for cells or other entities. A complementary paradigm gaining increasing traction is image-based profiling - quantifying many distinct…
Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
BlenderProc is a modular procedural pipeline, which helps in generating real looking images for the training of convolutional neural networks. These can be used in a variety of use cases including segmentation, depth, normal and pose…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
Providing high-quality electron images and hyperspectral X-ray maps is a focus of many modern electron microscopy laboratories. Nevertheless, further image processing and annotations are often needed to prepare them for publications and…
This paper presents the Container Profiler, a software tool that measures and records the resource usage of any containerized task. Our tool profiles the CPU, memory, disk, and network utilization of containerized tasks collecting over…
We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…
One major challenge in science is to make all results potentially reproducible. Thus, along with the raw data, every step from basic processing of the data, evaluation, to the generation of the figures, has to be documented as clearly as…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
KernelHaven is an open infrastructure for Software Product Line (SPL) analysis. It is intended both as a production-quality analysis tool set as well as a research support tool, e.g., to support researchers in systematically exploring…
This paper introduces the idea of mining container image repositories for configuration and other deployment information of software systems. Unlike traditional software repositories (e.g., source code repositories and app stores), image…
Feature extraction is a critical component of many applied data science workflows. In recent years, rapid advances in artificial intelligence and machine learning have led to an explosion of feature extraction tools and services that allow…
In recent years, a wide variety of automated machine learning (AutoML) methods have been proposed to search and generate end-to-end learning pipelines. While these techniques facilitate the creation of models for real-world applications,…
BrainLesion Suite is a versatile toolkit for building modular brain lesion image analysis pipelines in Python. Following Pythonic principles, BrainLesion Suite is designed to provide a 'brainless' development experience, minimizing…
$clustertools$ is a Python package for analyzing star cluster simulations. The package is built around the $StarCluster$ class, which stores all data read in from the snapshot of a given model star cluster. The package contains functions…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…