Related papers: CellProfiler Analyst 3.0: Accessible data explorat…
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that…
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…
Cellular image segmentation is essential for quantitative biology yet remains difficult due to heterogeneous modalities, morphological variability, and limited annotations. We present GenCellAgent, a training-free multi-agent framework that…
Increasing data set sizes of 3D microscopy imaging experiments demand for an automation of segmentation processes to be able to extract meaningful biomedical information. Due to the shortage of annotated 3D image data that can be used for…
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…
Datasets (semi-)automatically collected from the web can easily scale to millions of entries, but a dataset's usefulness is directly related to how clean and high-quality its examples are. In this paper, we describe and publicly release an…
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…
Photo Rater is a computer vision project that uses neural networks to help photographers select the best photo among those that are taken based on the same scene. This process is usually referred to as "culling" in photography, and it can…
Profiling data by plotting distributions and analyzing summary statistics is a critical step throughout data analysis. Currently, this process is manual and tedious since analysts must write extra code to examine their data after every…
Currently, food image recognition tasks are evaluated against fixed datasets. However, in real-world conditions, there are cases in which the number of samples in each class continues to increase and samples from novel classes appear. In…
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…
A wide range of scientific imaging datasets benefit from human inspection for purposes ranging from prosaic-such as fault identification and quality inspection-to profound, enabling the discovery of new phenomena. As such, these datasets…
Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical…
ConsumerCheck is an open source data analysis software tailored for analysis of sensory and consumer data. Since some of the implemented methods are generic, such as PCA, PLSR and PCR, other data from other domains may also be analysed with…
Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep…
We introduce CellSegmenter, a structured deep generative model and an amortized inference framework for unsupervised representation learning and instance segmentation tasks. The proposed inference algorithm is convolutional and…
Feature selection is used in machine learning to improve predictions, decrease computation time, reduce noise, and tune models based on limited sample data. In this article, we present FeatureExplorer, a visual analytics system that…
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…
In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step…
This article demonstrates a new conceptor network based classifier in classifying images. Mathematical descriptions and analysis are presented. Various tests are experimented using three benchmark datasets: MNIST, CIFAR-10 and CIFAR-100.…