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We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Backgr: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology.…
The reproducibility issue in science has come under increased scrutiny. One consistent suggestion lies in the use of scripted methods or workflows for data analysis. Image analysis is one area in science in which little can be done in…
We introduce ReservoirComputing.jl, an open source Julia library for reservoir computing models. The software offers a great number of algorithms presented in the literature, and allows to expand on them with both internal and external…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
Understanding how galaxies form and evolve requires measuring their light distributions in images taken by telescopes. This process often involves fitting mathematical models to galaxy images to extract properties such as size, brightness,…
We present the first public release of ShapePipe, an open-source and modular weak-lensing measurement, analysis, and validation pipeline written in Python. We describe the design of the software and justify the choices made. We provide a…
ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur…
Python is a particularly appealing language to carry out data analysis, owing in part to its user-friendly character as well as its access to well maintained and powerful libraries like NumPy and SciPy. Still, for the purpose of analyzing…
An open source symbolic tool for vector fields analysis 'SymFields' is developed in Python. The SymFields module is constructed upon Python symbolic module sympy, which could only conduct scaler field analysis. With SymFields module, you…
While constructing supervised learning models, we require labelled examples to build a corpus and train a machine learning model. However, most studies have built the labelled dataset manually, which in many occasions is a daunting task. To…
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…
Using a single tool to build and compare recommender systems significantly reduces the time to market for new models. In addition, the comparison results when using such tools look more consistent. This is why many different tools and…
Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physico-chemical…
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…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
This paper presents rerankers, a Python library which provides an easy-to-use interface to the most commonly used re-ranking approaches. Re-ranking is an integral component of many retrieval pipelines; however, there exist numerous…
MatchingTools is a Python library for doing symbolic calculations in effective field theory. It provides the tools to construct general models by defining their field content and their interaction Lagrangian. Once a model is given, the…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…