Related papers: Cellulyzer - Automated analysis and interactive vi…
Summary: Advances in 3D live cell microscopy are enabling high-resolution capture of previously unobserved processes. Unleashing the power of modern machine learning methods to fully benefit from these technologies is, however, frustrated…
We describe Ganalyzer, a model-based tool that can automatically analyze and classify galaxy images. Ganalyzer works by separating the galaxy pixels from the background pixels, finding the center and radius of the galaxy, generating the…
Parallel algorithms for solving any image processing task is a highly demanded approach in the modern world. Cellular Automata (CA) are the most common and simple models of parallel computation. So, CA has been successfully used in the…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
Tracking individual cells in live-cell imaging provides fundamental insights, inevitable for studying causes and consequences of phenotypic heterogeneity, responses to changing environmental conditions or stressors. Microbial cell tracking,…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unbiased measurements that reveal phenotypic patterns powerful…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
We present BrainPainter, a software that automatically generates images of highlighted brain structures given a list of numbers corresponding to the output colours of each region. Compared to existing visualisation software (i.e.…
We present JDLL, an agile Java library that offers a comprehensive toolset/API to unify the development of high-end applications of DL for bioimage analysis and to streamline their installation and maintenance. JDLL provides all the…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
A human watching a video of closely-packed cells can generally identify every individual cell, regardless of density and noise, but most currently-available cell-tracking software cannot. This is because the human brain automatically builds…
This work discusses preliminary work aimed at simulating and visualizing the growth process of a tiny structure inside the cell---the microtubule. Difficulty of recording the process lies in the fact that the tissue preparation method for…
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…
Cellular automata are a class of computational models based on simple rules and algorithms that can simulate a wide range of complex phenomena. However, when using conventional computers, these 'simple' rules are only encapsulated at the…
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…