Package for interacting with Bio-Formats library in the Wolfram Language
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BioFormatsLink
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CONTRIBUTING.md
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README.md
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README.md

BioFormatsLink for Wolfram Language

BioFormatsLinkLogo

BioFormatsLink is a package for interacting with Bio-Formats library in the Wolfram Language. BioFormatsLink supports 10.2 and later versions of Wolfram Language deployments for the desktop, including Wolfram Desktop and 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.
  • You may want to modify the value of $versionNumber variable.
  • 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. 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: