MicroJSON is a JSON-based format inspired by GeoJSON, designed to encode a variety of data structures related to microscopy images. It can handle representations of reference points, regions of interest, and other annotations, making it an ideal solution for conveying complex microscopy data in a straightforward, easy-to-use format.
For more extensive documentation, please refer to the online documentation.
MicroJSON offers a range of features designed to meet the needs of microscopy data representation:
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Flexible Data Structures: MicroJSON can represent diverse data structures, including geometries (such as points, multipoints, linestrings, polygons), features (individual entities with specific properties), feature collections (groups of features), and coordinate systems.
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Standardized Format: MicroJSON uses the widely adopted JSON format, ensuring compatibility with a wide range of programming languages and tools.
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Extensibility: MicroJSON can handle additional properties associated with specific features, such as metadata relating to microscopy images.
There are two additional functionalities added which supports binary and label images.
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OmeMicrojsonModel: Converts objects in a binary or label images into polygon coordinates (rectangle, encoding) and save them in json file format using microjson package.
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MicrojsonBinaryModel: Reconstruct binary images using polygon coordinates from json file.
To install MicroJSON, you can use the following command:
pip install microjsonThis will install the default version of MicroJSON with the basic functionalities and minimal dependencies. If you want to use the additional functionalities, such as provided by the utils module, you can install the package with the following command:
pip install microjson[all]MicroJSON is compatible with any application or tool that process JSON data. Its design makes it especially well-suited for applications involving analysis, visualization, and manipulation of microscopy images.
Refer to the examples foler to see samples of MicroJSON files as well as a simple parsing example, or the example in the documentation
For more detailed information about the MicroJSON structure and its components, please refer to the Specification file.
The GeoJSON test files are copied from the GeoJSON Schema GitHub repository, and are Copyright (c) 2018 Tim Schaub under MIT License.
We welcome contributions to the development and enhancement of MicroJSON. Whether you're reporting bugs, suggesting enhancements, or contributing to the code, your input is highly appreciated.
MicroJSON is licensed under MIT License.
This project is maintained by Polus AI. For any queries or further discussion, please contact [contact details].
