wolframresearch / bioformatslink

Package for interacting with Bio-Formats library in the Wolfram Language

BioFormatsLink for Wolfram Language

BioFormatsLink is a package for interacting with Bio-Formats library in the Wolfram Language. BioFormatsLink supports 12.1 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.
• 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:

• LICENSE.txt - BioFormatsLink license
• CONTRIBUTING.md - Guidelines for contributing to BioFormatsLink

bioformatslink's Issues

Importing larger CZI files fail

Hi,

I'm use BioFormatsLink to import .czi images (containing a single image with two channels), and it works fine for images that are 4915x4915 pixels in dimension. However, when I try and import an image that is 6861x6861, I get $Failed.

Going into the BioFormatsLink code and removing the Quiet's that are littered everywhere tells me that Java is running out of memory. It would be helpful if at least this error was not silenced.

If I make a copy of the BioFormatsLink.wl file and increase the Java heap size via ReinstallJava[JVMArguments -> "-Xmx1g"] it works fine (which is my current workaround), but if I try and do the same when calling Needs["BioFormatsLink`"] either before or after, the importing now fails for all my czi images.