0.4.0 - ABBA extension for QuPath 0.6.*

This release makes this extension compatible with QuPath 0.6.

The extension can be installed through the PTBIOP catalog:

https://github.com/BIOP/qupath-biop-catalog

Note that the BraiAn extension is available via another catalog:

https://github.com/carlocastoldi/qupath-extension-braian-catalog

0.3.3 - ABBA extension for QuPath 0.5.*

This release is probably the last one to officially support QuPath 0.5.+.

• fix a bug from v0.3.2 that forbid importing Waxholm Rat Atlas annotations (see #29)
• licence changed from Apache 2.0 to MIT
• API changes
  • loading annotations can now overwrite any previous previous import of the same atlas version. Overwrite will only work if the previous atlas's hierarchy wasn't disrupted (i.e. everything is still a child of "Root", see #19)
  • AtlasTools.loadWarpedAtlasAnnotations() now returns the "Root" annotation
  • the "Root" annotation is now locked and classified with the name of the atlas version
  • "Load Atlas Annotations Into Open Image" command in GUI now lets you select the atlas to import, if multiple were exported from ABBA (see #29)
  • deprecated AtlasTools.loadWarpedAtlasAnnotations() interface that chose unpredictably the atlas to import, if multiple were exported from ABBA. This is in favour of more explicit interfaces that require to give the name of the atlas or the AtlasOntology itself (see #29)
  • removes atlasName parameter from functions requiring the ontology too. The old API is deprecated
  • removed calls to deprecated QuPath functions
• removed dependency on QuPathGUI (see #24).
  This allows to use the extension in CLI environments such as with PAQUO.

Full Changelog: 0.3.1...0.3.3

0.3.2 - ABBA extension for QuPath 0.5.*

NOTE: DO NOT WORK WITH Rat Atlases (and maybe other ones)

• licence changed from Apache 2.0 to MIT
• API changes
  • loading annotations can now overwrite any previous previous import of the same atlas version. Overwrite will only work if the previous atlas's hierarchy wasn't disrupted (i.e. everything is still a child of "Root", see #19)
  • AtlasTools.loadWarpedAtlasAnnotations() now returns the "Root" annotation
  • the "Root" annotation is now locked and classified with the name of the atlas version
  • removes atlasName parameter from functions requiring the ontology too. The old API is deprecated
  • removed calls to deprecated QuPath functions
• removed dependency on QuPathGUI (see #24).
  This allows to use the extension in CLI environments such as with PAQUO.

ABBA Extension 0.3.1 for QuPath 0.5

• Bug fix when importing with left and right split and ID property
• Better error message when no registration was exported
• Removes package issue in example scripts

ABBA Extension for QuPath 0.5

QuPath 0.5.0 compatibility

• template scripts added
• removes deprecated API thanks to @carlocastoldi

ABBA Extension v0.1.4 for QuPath 0.3+ and QuPath 0.4+

This release fixes a bug whereby the transformation of transformed image server was not taken into account in AtlasTools.getAtlasToPixelTransform(getCurrentImageData())

(thanks Olexiy!)

ABBA Extension v0.1.3 for QuPath 0.3+

More convenient API for AtlasTools
Loading the annotation creates a recordable QuPath workflow step
Better handling of error when no registration is available

(alpha feature : builder pattern for atlas loader, see AtlasImporter)

ABBA Extension for QuPath 0.3+

QuPath extension for the Aligning Big Brains and Atlases workflow (https://github.com/BIOP/ijp-imagetoatlas)

To install the extension: unzip jars files contained in the zip files then drag and drop them into QuPath v0.3+

On windows, you may need to delete obsolete files manually.

Bug fix added on v0.1.2:

• correct handling of left right regions import with QuPath rotated image servers (thanks to Olexiy Kochubey)

ABBA Extension for QuPath 0.3.0

Unzip jars files contained in the zip files then drag and drop them into QuPath 0.3.0

ABBA Extension preview version for QuPath 0.3.0

Drag and drop the jar into QuPath to install the extension.

Currently works only for Mouse Atlas CCFv3