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https://github.com/WolframResearch/BioFormatsLink

Package for interacting with Bio-Formats library in the Wolfram Language
https://github.com/WolframResearch/BioFormatsLink

bio-formats java jlink library mathematica microscopy wolfram-language

Last synced: about 2 months ago
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Package for interacting with Bio-Formats library in the Wolfram Language

Host: GitHub
URL: https://github.com/WolframResearch/BioFormatsLink
Owner: WolframResearch
License: gpl-2.0
Created: 2017-09-29T14:50:45.000Z (almost 7 years ago)
Default Branch: master
Last Pushed: 2022-11-29T13:03:29.000Z (almost 2 years ago)
Last Synced: 2024-07-18T20:45:40.325Z (2 months ago)
Topics: bio-formats, java, jlink, library, mathematica, microscopy, wolfram-language
Language: Mathematica
Homepage:
Size: 66.6 MB
Stars: 15
Watchers: 21
Forks: 8
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt

Awesome Lists containing this project

awesome-wolfram-language - BioFormatsLink - Formats library in the Wolfram Language. (Bioinformatics)

README

        # BioFormatsLink for Wolfram Language

![BioFormatsLinkLogo](logo.png)

BioFormatsLink is a package for interacting with [Bio-Formats](http://www.openmicroscopy.org/bio-formats/) library in the [Wolfram Language](https://www.wolfram.com/language/). BioFormatsLink supports 12.1 and later versions of Wolfram Language deployments for the desktop, including [Wolfram Desktop](https://www.wolfram.com/desktop/) and [Mathematica](https://www.wolfram.com/mathematica/).

### Building BioFormatsLink

    

To build a `.paclet` file:

* Build documentation using Ant's script in Scripts/docbuild.xml.

* Open Scripts/assemblePaclet.wl in the Wolfram system.

* Run the entire package.

* The `.paclet` file will be created in `/full/path/to/BioFormatsLink/build/date-time` directory.

### Installing the BioFormatsLink release

The BioFormatsLink release comes in the form of a `.paclet` file, which contains the entire package and its documentation. Download the latest release from the [Github repo's releases page](https://github.com/WolframResearch/BioFormatsLink/releases). To install, run the following command in the Wolfram Language:

    PacletInstall["/full/path/to/BioFormatsLink-version.paclet"]

This will permanently install the BioFormatsLink paclet. The Wolfram Language will always use the latest installed version of BioFormatsLink. Installed versions can be enumerated using the command:

    PacletFind["BioFormatsLink"]

And all versions can be uninstalled using the command:

    PacletUninstall["BioFormatsLink"]

    

 

### Using BioFormatsLink

To access the documentation, open the notebook interface help viewer, and search for BioFormatsLink/tutorial/ImportingDataFromBioFormats. This will open a tutorial on how to import data using BioFormatsLink.

To start, load the BioFormatLink package, and try opening an image file.

    Needs["BioFormatsLink`"]

    Import["ExampleData/spikey.tiff", "BioFormats"] 

    

### More...

See the following files for more information:

* [LICENSE.txt](LICENSE.txt) - BioFormatsLink license

* [CONTRIBUTING.md](CONTRIBUTING.md) - Guidelines for contributing to BioFormatsLink