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{mu}Manager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely coupled. This is because {mu}Manager libraries are written in C++ and Java, whereas image processing is increasingly carried out with data science and machine learning tools most easily accessible through the Python programming language. We present Pycro-Manager, a tool that enables rapid development of such experiments, while also providing access to the wealth of existing tools within {mu}Manager through Python.
Transition from conventional to digital pathology requires a new category of biomedical informatic infrastructure which could facilitate delicate pathological routine. Pathological diagnoses are sensitive to many external factors and is known to be s
We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii) perform repr
Central nervous system (CNS) tumors come with the vastly heterogeneous histologic, molecular and radiographic landscape, rendering their precise characterization challenging. The rapidly growing fields of biophysical modeling and radiomics have shown
Development organizations and International Non-Governmental Organizations have been emphasizing the high potential of Free and Open Source Software for the Less Developed Countries. Cost reduction, less vendor dependency and increased potential for
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run large genomi