Related papers: SCIMAP: A Python Toolkit for Integrated Spatial An…

Multiplexed immunofluorescence microscopy captures detailed measurements of spatially resolved, multiple biomarkers simultaneously, revealing tissue composition and cellular interactions in situ among single cells. The growing scale and…

Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…

Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells are largely based on transcriptomic single-cell…

Quantitative characterization of cellular spatial organization is critical for understanding tumor progression and immune response. Recent advances in artificial intelligence (AI) enable large-scale segmentation and classification of nuclei…

The CMAP (cultural mapping and pattern analysis) visualization toolkit introduced in this paper is an open-source suite for analyzing and visualizing text data - from qualitative fieldnotes and in-depth interview transcripts to historical…

The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial…

Recent developments in spatial omics technologies have enabled the generation of high dimensional molecular data, such as transcriptomes, proteomes, and epigenomes, within their spatial tissue context, either through coprofiling on the same…

Medical image analysis plays a key role in precision medicine as it allows the clinicians to identify anatomical abnormalities and it is routinely used in clinical assessment. Data curation and pre-processing of medical images are critical…

Spatial Transcriptomics (ST) enables the measurement of gene expression while preserving spatial information, offering critical insights into tissue architecture and disease pathology. Recent developments have explored the use of…

Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in…

Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…

Scipp is heavily inspired by the Python library xarray. It enriches raw NumPy-like multi-dimensional arrays of data by adding named dimensions and associated coordinates. Multiple arrays are combined into datasets. On top of this, scipp…

Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…

We present the open-source image processing software package PySAP (Python Sparse data Analysis Package) developed for the COmpressed Sensing for Magnetic resonance Imaging and Cosmology (COSMIC) project. This package provides a set of…

This paper presents evomap, a Python package for dynamic mapping. Mapping methods are widely used across disciplines to visualize relationships among objects as spatial representations, or maps. However, most existing statistical software…

This paper is an overview of Image Processing and Analysis using Scilab, a free prototyping environment for numerical calculations similar to Matlab. We demonstrate the capabilities of SIP -- the Scilab Image Processing Toolbox -- which…

Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…

Early identification of a polyp in the lower gastrointestinal (GI) tract can lead to prevention of life-threatening colorectal cancer. Developing computer-aided diagnosis (CAD) systems to detect polyps can improve detection accuracy and…

Recent advances in multiplex imaging have enabled researchers to locate different types of cells within a tissue sample. This is especially relevant for tumor immunology, as clinical regimes corresponding to different stages of disease or…