A PyTorch framework for classification and regression of images, volumes, timeseries and videos including various finetuning methods and training from scratch strategies.

This repository contains an easy-to-use and flexibly customizable framework for developing and training semantic segmentation models. The focus was put on being usable out-of-the-box, without being a black box and giving the possibility to be adapted to individual projects. Therefore several features like pre-trained state-of-the-art models are already provided for …

CrystFEL is a suite of programs for processing serial crystallography data. CrystFEL comprises programs for indexing and integrating diffraction patterns, scaling and merging intensities, simulating patterns, calculating figures of merit for the data and visualising the results.

DigitalMicrograph® is software for (scanning) transmission electron microscope ((S)TEM) experimental control and analysis, which people also know as Gatan Microscopy Suite® (GMS).

Gatan on DigitalMicrograph

A visual node-based workflow system for automated microscopy image analysis, segmentation, and plankton classification using computer vision and deep learning. No coding required.

The Dislocation Ontology Suite (DISOS) is an ontology suite comprising several modules describing materials scientific concepts, representations of dislocations, and different simulation models in the dislocation domain. Currently, DISOS comprises three ontologies, including:

• Dislocation Ontology (DISO)
• Crystal Structure Ontology (CSO)
• Crystallographic Defect Ontology (CDO)

DiversityScanner is a sorting robot that prepares specimens from bulk samples for barcoding to study invertebrate biodiversity. It detects, images and measures individual specimens from a sample and then moves them into the wells of a 96-well microplate.

For more infos see: DiversityScanner: Robotic handling of small invertebrates with machine …

Drishti is an open-source scientific visualisation software designed by Ajay Limaye at the National Computational Infrastructure's VizLab.
 
The central idea of Drishti is that scientists can use it to explore and present volumetric datasets without extensive training.
 
Drishti has been developed with its end use in mind: ie. visualising volumetric …

Python package for rendering netCDF map over time as a video using PyVista.

With the EM glossary initiative, our goal is to harmonize terminology in the field of electron and ion microscopy so humans, devices and algorithms can exchange data easily and collaborate more efficiently and effectively.

We achieve this through the following measures:

1. moderation of a community collaboratively harmonising terminology,
2. provision of …

EnPT - EnMAP Processing Tool

The Environmental Mapping and Analysis Program (EnMAP) is a German hyperspectral satellite mission that aims at monitoring and characterising the Earth’s environment on a global scale. The EnPT Python package is an automated pre-processing pipeline for the new EnMAP hyperspectral satellite data. It provides free …

Build your own plug-in Entomoscope and use the ENIMAS (Entomoscope Imaging Software) here

Eventdisplay is a reconstruction and analysis pipeline for data of Imaging Atmospheric Cherenkov Telescopes (IACT).
It has been primarily developed for VERITAS and CTAO analysis.

The Eventdisplay package consists of several analysis steps and tools:

1. evndisp: calibrate and parametrize images, event reconstruction, stereo analysis
2. trainTMVAforAngularReconstruction: train boosted decision …

FastSurfer is a fast and accurate deep-learning based neuroimaging pipeline for the automated processing of structural human brain MRIs. Based on a T1-weighted MRI you get everything you need for quick structure localization (whole brain segmentation in under 1 minute), extraction of quantitative measures, …

FatSegNet : A Fully Automated Deep Learning Pipeline for Adipose Segmentation on Abdominal Dixon MRI

This repository contains the tool designed for the Rhineland Study
for segmenting visceral and subcuteneous adipose tissue on fat
images from a two-point Dixon sequence.

If you use this tool please cite:

Estrada, Santiago, et …

This repository contains a framework for benchmarking failure detection methods under distribution shifts in image classification featuring implementations of baseline methods, data sets and metrics. Additionally to a wide range of built-in methods, this framework can be used to evaluate and compare new methods, models and datasets.

FESOM (Finite-Element/volumE Sea ice-Ocean Model) is a multi-resolution sea ice-ocean model that solves the equations of motion on unstructured meshes. The model is developed and supported by researchers at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), in Bremerhaven, Germany.

See also

FESOM home page

Python package for colocalization of RS-FISH results with either RS-FISH results (e.g from two image channels) 2D/3D, or with an image (only 2D for now).

FishInspector

Screenshot of FishInspector Software Version 1.03

The FishInspector software allows the user-friendly and easy annotation of features in zebrafish embryo 2-dimensional images. Features are detected automatically but may require correction by the user (implemented in the software). At present only lateral images can be analysed, but the software could …

FracSPy offers a complete, user-friendly solution for microseismic processing. Designed for accessibility, FraCSPy integrates existing Python libraries into modular workflows, enabling users to manage the entire processing pipeline — from detection to event characterisation — with ease. By making established techniques broadly available, FraCSPy fosters innovation, education, and benchmarking within …

fsqc toolbox

Description

This package provides quality assurance / quality control scripts for FastSurfer- or
FreeSurfer-processed structural MRI data. It will check outputs of these two software
packages by means of quantitative and visual summaries. Prior processing of data using
either FastSurfer or FreeSurfer is required, i.e. the software cannot …