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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…
Biomedical photoacoustic tomography, which can provide high resolution 3D soft tissue images based on the optical absorption, has advanced to the stage at which translation from the laboratory to clinical settings is becoming possible. The…
Fourier Ptychographic Microscopy (FPM) is a computational imaging technique that enables high-resolution imaging over a large field of view. However, its application in the biomedical field has been limited due to the long image…
Telegram is a popular platform for public communication, generating large amounts of messages through its channels. pytopicgram is a Python library that helps researchers collect, organize, and analyze these Telegram messages. The library…
Fourier transforms are an often necessary component in many computational tasks, and can be computed efficiently through the fast Fourier transform (FFT) algorithm. However, many applications involve an underlying continuous signal, and a…
Ptychography is now integrated as a tool in mainstream microscopy allowing quantitative and high-resolution imaging capabilities over a wide field of view. However, its ultimate performance is inevitably limited by the available coherent…
We present PyTorch Connectomics (PyTC), an open-source deep-learning framework for the semantic and instance segmentation of volumetric microscopy images, built upon PyTorch. We demonstrate the effectiveness of PyTC in the field of…
We introduce \texttt{pycobra}, a Python library devoted to ensemble learning (regression and classification) and visualisation. Its main assets are the implementation of several ensemble learning algorithms, a flexible and generic interface…
In this paper, we present OpenMedIA, an open-source toolbox library containing a rich set of deep learning methods for medical image analysis under heterogeneous Artificial Intelligence (AI) computing platforms. Various medical image…
Fourier ptychography has attracted a wide range of focus for its ability of large space-bandwidth-produce, and quantative phase measurement. It is a typical computational imaging technique which refers to optimizing both the imaging…
Photon-HDF5 is an open-source and open file format for storing photon-counting data from single molecule microscopy experiments, introduced to simplify data exchange and increase the reproducibility of data analysis. Part of the Photon-HDF5…
This work presents the new template matching capabilities implemented in Pyxem, an open source Python library for analyzing four-dimensional scanning transmission electron microscopy (4D-STEM) data. Template matching is a brute force…
Leveraging medical record information in the era of big data and machine learning comes with the caveat that data must be cleaned and de-identified. Facilitating data sharing and harmonization for multi-center collaborations are…
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…
We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…
scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented…
BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…
Simulation of atomic resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…