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github.com/BIOP/qupath-extension-warpy @0.5.0

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README

QuPath Warpy extension

This repo adds some support for nonlinear deformation and registration in QuPath, by using the ImgLib2 library.

Documentation

https://imagej.net/plugins/bdv/warpy/warpy

Installing

In QuPath 0.6, this extension should be installed via the QuPath BIOP catalog.

Don't forget to restart QuPath (but not your computer).

Citing

https://doi.org/10.3389/fcomp.2021.780026

Building

You can build the QuPath Warpy extension from source with

gradlew clean build

The output will be under build/libs.

clean removes anything old
build builds the QuPath extension as a .jar file and adds it to libs

Core symbols most depended-on inside this repo

getName

called by 30

src/main/java/qupath/ext/imagecombinerwarpy/ImageCombinerWarpyExtension.java

build

called by 18

src/main/java/qupath/ext/imagecombinerwarpy/gui/RealTransformImageServerBuilder.java

getMetadata

called by 17

src/main/java/qupath/ext/imagecombinerwarpy/gui/RealTransformImageServerBuilder.java

apply

called by 14

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/BoundedRealTransform.java

getAffine

called by 13

src/main/java/qupath/ext/imagecombinerwarpy/gui/ImageCombinerWarpyServerOverlay.java

serialize

called by 11

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/RealTransformSerializer.java

deserialize

called by 10

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/RealTransformSerializer.java

getName

called by 7

src/main/java/qupath/ext/warpy/WarpyExtension.java

Shape

Method 172

Class 33

Enum 3

Languages

Java100%

Modules by API surface

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/RealTransformSerializer.java35 symbols

src/main/java/qupath/ext/imagecombinerwarpy/gui/ImageCombinerWarpyPane.java31 symbols

src/main/java/qupath/ext/warpy/Warpy.java16 symbols

src/main/java/qupath/ext/imagecombinerwarpy/gui/RealTransformImageServer.java11 symbols

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/BoundedRealTransform.java10 symbols

src/main/java/qupath/ext/imagecombinerwarpy/gui/AffineTransformInterpolationImageServer.java10 symbols

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/Wrapped2DTransformAs3D.java9 symbols

src/main/java/qupath/ext/imagecombinerwarpy/realtransform/InvertibleWrapped2DTransformAs3D.java9 symbols

src/main/java/qupath/ext/imagecombinerwarpy/gui/RealTransformInterpolation.java9 symbols

src/main/java/qupath/ext/imagecombinerwarpy/ImageCombinerWarpyExtension.java9 symbols

src/main/java/qupath/ext/warpy/WarpyExtension.java8 symbols

src/main/java/qupath/ext/imagecombinerwarpy/gui/RealTransformImageServerBuilder.java7 symbols

For agents

$ claude mcp add qupath-extension-warpy \
  -- python -m otcore.mcp_server <graph>

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