Efficient Annotation of Plankton images by Clustering

This repository contains a framework which allows for enhanced model interpretability and model robustness. The framework utilizes interpretable disentangled representations for downstream-task prediction which are in a second step visualized and evaluated through a multipath-attribution mapping.

MultiSat4Slows closes the loop between automated landslide detection and human interpretation by enabling users to explore, validate, and iteratively refine analytical results through interactive Visual Analytics methods.

Nanomegas on ACOM

Segment anything with our Napari integration of Meta AI's new Segment Anything Model (SAM)!

SAM is the new segmentation system from Meta AI capable of one-click segmentation of any object, and now, our plugin neatly integrates this into Napari.

We have already extended SAM's click-based foreground separation to full click-based …

Nexus - Nuclear Elastic X-ray scattering Universal Software

The Nuclear Elastic X-ray scattering Universal Software (NEXUS) is a Python package for simulating and fitting of

• Moessbauer spectra
• nuclear resonant scattering (NRS) quantum beats
• pure electronic X-ray reflectivities (XRR)
• nuclear X-ray reflectivities (nXRR)
• polarization dependent electronic scattering.

Documentation

https://fs-mcp.pages.desy.de/nuclear-nexus/ …

Simultaneous localisation and categorisation of objects, also referred to as object detection, is of high relevance for many applications which rely on rating of objects rather than e.g. pixels or entire images. For this task, the cumbersome and iterative process of method configuration constitutes a major research and application bottleneck. …

Analyzing complex 3D image data is essential across many research fields, but existing tools are often slow, difficult to use, and limited in flexibility. Our solution, nnInteractive, makes this process simple and efficient by allowing users to interact with images using intuitive actions like clicks, scribbles, boxes, or freehand selections. …

When confronted with a new dataset, the application of AI-based segmentation methods is non-trivial. Substantial manual effort is required to optimize the network topology, preprocessing, training procedure and inference strategy to the task at hand. Such adaptations are non-trivial and require substantial expertise to ensure optimal performance on each dataset. …

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 …

Collection of neural network models for automatic image segmentation of microscopic tumor spheroids. Intended to be used with nnU-Net deep-learning framework. Trained and tested on a total of microscopic images of mouse pheochromocytoma (MPC) tumor cells.

In addition to the trained network model, a PyQt5-based graphical user interface tool is …

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 …