Micro-Meta App - React implementation

Micro-Meta App is an intuitive Graphical User Interface (GUI)-based open-source software that helps scientists to interactively build graphical representations of microscope hardware by dragging-and-dropping individual components onto the workspace and entering the relevant attribute values based on the 4D Nucleome (4DN) - BioImaging North America (BINA) Microscopy Metadata guidelines that scale experimental complexity. From this, Micro-Meta App automatically generates structured Microscope files that can be saved locally, consumed by existing data portals, shared with other scientists, and used repeatedly whenever the same microscope is used to produce image data. Thus, when the image acquisition settings utilized to produce a given image dataset need to be recorded, the user selects the desired image data alongside the relevant Microscope file. Then, Micro-Meta App imports the relevant metadata from the header of image data files to be annotated and interactively guides the user through the collection of all missing attributes. Finally, the App generates a Settings-file, which coupled with the Microscope-file contains comprehensive descriptions of the conditions utilized to produce individual microscopy datasets.If you use this software please cite both the software using the metadata indicated below, and the papers as indicated in the scope of each referenc

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

AbstractThe 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (https://data.4dnucleome.org/), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.</jats:p

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes