v0.0.7

Many changes, fixes and improvements - most notably support for 32-bit images, including Perkin Elmer multichannel TIFFs processed by InForm (part of the Bio-Formats sample data).

This extension version has been more extensively tested across a wider range of images than ever before, including ones that were previously problematic, but please do be on the lookout for bugs.

Note that the methods of parsing the objective magnification and downsample factors for different layers of the image pyramid have changed; the new approaches are expected to be more robust, but please report any problems.

Also, it would be a good time to clean out your QuPath extensions directory, updating to the latest version of bioformats_package.jar and this extension. Make sure to delete any older versions (including v0.0.6, which unfortunately has a different filename and so won't be overwritten automatically). If you go to Help → Installed extensions you should now see the version number of the Bio-Formats library that you have installed.

• New calculation of downsample factors
• Support for 32-bit floating point images
• 8-bit indexed color images no longer fail, but treated as regular 8-bit (necessary for some .lif files)
• Revised parsing of z/t values
• New dumpMetadata() method to access OME-XML to help with debugging
• New getChannelName(channel) method
• Introduced DummyMetadata() when creating secondary readers for multithreading
• Removed autoscaling with use of non-RGB getBufferedThumbnail
• Improved parsing of objective magnification
• Added new code to test QuPath's use of Bio-Formats
• Added Bio-Formats version number under 'Help → Installed extensions'
• An error is shown when starting QuPath is 'bioformats_package.jar' is missing

v0.0.6

Several bug-fixes, mostly around how channels are handled:

• Added fix where 4-channel 8-bit images could be converted to RGB, losing the 4th channel information for some commands (qupath/qupath#164)
• Added workaround for VSI reading bug that meant channels & z-slices were sometimes confused (available in preferences, turned off by default)
• Added fix where some formats (e.g..ims) would have 8-bit RGB data, but this was treated as multichannel; now such cases are treated as packed (A)RGB, giving better performance & more consistent behavior

This version also introduces using Gradle rather than Maven. For more information about the benefits of this switch for QuPath generally, see this blog post.

v0.0.5

• Fixes bug where multiplex images having > 4 channels would not open property (described at qupath/qupath#145)
• Improves preferences & control over generation of .bfmemo files (see Google Groups discussion here)
• Improved ReadMe.md to describe the various preferences.
• Adds experimental option to parallelize requests for multiple channels of a multichannel image

v0.0.4

This is a major revision incorporating many bug-fixes and performance improvements, including:

• Much better support for a range of image types, especially CZI, NDPIS and VSI
• Bio-Formats' memoization can now be used to improve performance when (re)opening images
• Improved parallelization when reading image tiles - should be faster, require less memory, and turn itself off when it would do more harm than good
• A new set of Bio-Formats options have been added to the QuPath preference panel, including the ability to always use/skip Bio-Formats when opening images with specific file extensions

More details here.

Note: memoization involves writing a (hidden) cache file whenever an image is opened. This is stored alongside the original image file, in the same directory. If you don’t like that, you can either request a different directory or turn of memoization altogether.

v0.0.3

Several more bug fixes, mostly for help in thumbnail generating with QuPath v0.0.6 and above.

Version 0.0.3

• Fixed bug when resizing image regions

v0.0.2

Several important bugs fixed, most notably:

• Fixed bugs that prevented reading non-RGB whole slide images
• Added nearest-neighbor interpolation method to fix accidental intensity rescaling if resized image regions were requested

Warning! The QuPath Bio-Formats extension is still incomplete, and requires more development and testing.

Currently, it works well for some file formats, but not yet for all the formats that Bio-Formats usually supports.

More work is needed to ensure that QuPath interprets the Bio-Formats metadata correctly.

v0.0.1

First pre-release of QuPath Bio-Formats Extension - intended for testing only