ObiWan-Microbi: OMERO-based integrated Workflow for annotating Microbes in the Cloud

ObiWan-Microbi is a toolkit collection for semi-automated segmentation and annotation of (biological) time-lapse image data in the cloud. It utilizes an OMERO image server for data management. We contribute SegUI - a browser-based tool for semi-automated manual segmentation and annotation …

For the understanding of the dynamics inside crowds reliable empirical data are needed enabling an increase of safety and comfort for pedestrians and the design of models reflecting the real dynamics. Manual procedures for collecting this data are very time-consuming and usually do not supply sufficient accuracy in space and …

PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms

PickYOLO is a super-fast, universal particle detector, based on the deep-learning real-time object recognition system YOLO (You Only Look Once). After training with the centre coordinates of a few hundred representative particles, the network automatically detects additional particles …

PixelPatrol is a tool designed for the systematic validation of scientific image datasets. It helps researchers proactively assess their data before engaging in computationally intensive analysis, ensuring the quality and integrity of datasets for reliable downstream analysis.

Polarityjam is a software suite to study endothelial cell behavior and more. Visit https://polarityjam.readthedocs.io/en/latest/index.html for more informations!

The VLBI data analysis software PORT estimates Earth orientation parameters, radio telescope and radio source coordinates, as well as other, auxiliary parameters employing weighted least-squares estimation. PORT is designed to process VGOS observations, as well as traditional S-/X-band and single-band observations, regardless of data length. PORT processes both Intensive and …

preCICE is an open-source coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations.

Partitioned means that preCICE couples existing programs/solvers capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is …

When using light with short wavelengths, such as in the extreme ultraviolet (EUV) regime, conventional focusing optics are no longer practical due to strong material absorption and fabrication limitations. Instead, the sample is scanned, and diffraction patterns are recorded directly behind it. Using numerical reconstruction algorithms, both the amplitude and …

Conventional (CP) and Fourier (FP) ptychography have emerged as versatile quantitative phase imaging techniques. While the main application cases for each technique are different, namely lens-less short wavelength imaging for CP and lens-based visible light imaging for FP, both methods share a common algorithmic ground. CP and FP have in …

pyDIDAS (python DIffraction Data Analysis Suite) is a toolset developed at Helmholtz-Zentrum Hereon to improve the ease of use and efficiency of diffraction data analysis. A key requirement is to create a graphical user interface of the software and processing which scales with available resources to allow running pyDIDAS on …

PyPlaque

We introduce PyPlaque, an open-source Python package focusing on flexibility and modularity rather than a bulky graphic user interface. Unlike previous methods, an abstracted architecture using object-oriented programming allows accommodation of various experimental containers and specimen carriers as data structures while focusing on phenotype-specific information. Aligned with the logical …

RAYX is a simulation tool for beamlines at electron storage rings. It traces synchrotron radiation through a series of mirrors, gratings and more and provides the user with helpful insights, how a given beamline performs.

Reflectorch is a Python package for the analysis of X-ray and neutron reflectivity data using Pytorch-based neural networks developed by the Schreiber Lab in Tübingen, Germany.

The training pipeline incorporates prior boundaries for the thin film parameters as an additional input to the neural network alongside the reflectivity curves. This …

Standard neural networks for imaging tasks are tied to a certain fixed image resolution they were trained on. Neural operators were proposed in Kovachki, Nikola, et al. “Neural operator: Learning maps between function spaces with applications to PDEs” as a way to generalize neural networks to an infinite-dimensional setting. A …

Open-source InSAR time series analysis software developed within the project SAR4Infra. SARvey aims to analyze InSAR displacement time series for engineering applications.

How to cite

If you use SARvey in your research, please cite the following.

1. The paper describing the methodology:

Piter A, Haghshenas Haghighi M, Motagh M (2024). Challenges …

Sen12Landslides is a large-scale, multi-modal dataset featuring 75,000 annotations from Sentinel-1/2 timeseries and DEM data designed to advance spatio-temporal landslide detection and geohazard monitoring. By providing precise pre- and post-event imagery across 15 global regions, it enables deep learning models to capture the complex temporal dynamics of landslide behavior.

2D image registration tool using CV2 SIFT.

The toolkit for Simulation and Image Processing for Photonics and Acoustics (SIMPA)

SIMPA aims to facilitate realistic image simulation for optical and acoustic imaging modalities by
providing adapters to crucial modelling steps, such as volume generation; optical modelling; acoustic
modelling; and image reconstruction. SIMPA provides a communication layer between various …

The solar wind is constituted by plasma and radiation emitted by the Sun and it can have adverse effects on power grids, telecommunication infrastructure and space assets. In particular during late October-November 2003, geomagnetic storms (popularly known as “Halloween storms”) resulted in numerous satellite anomalies, including the rerouting of transpolar …

Syris (synchrotron radiation imaging simulation) is a framework for simulations of X-ray absorption and phase contrast dynamic imaging experiments, like time-resolved radiography, tomography or laminography. It includes X-ray sources, various sample shape creation possibilities, complex refractive index lookup options, motion model and indirect detection model …

The increasing use of deep learning techniques has reduced interpretation time and, ideally, reduced interpreter bias by automatically deriving geological maps from digital outcrop models. However, accurate validation of these automated mapping approaches is a significant challenge due to the subjective nature of geological mapping and the difficulty in collecting …