https://github.com/qupath/qupath-imglib2

A Java library to link QuPath and ImgLib2
https://github.com/qupath/qupath-imglib2

Last synced: 5 months ago
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A Java library to link QuPath and ImgLib2

• Host: GitHub
• URL: https://github.com/qupath/qupath-imglib2
• Owner: qupath
• License: apache-2.0
• Created: 2025-09-24T09:29:46.000Z (8 months ago)
• Default Branch: main
• Last Pushed: 2026-01-16T16:44:07.000Z (5 months ago)
• Last Synced: 2026-01-17T05:26:38.333Z (5 months ago)
• Language: Java
• Size: 238 KB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# QuPath-imglib2

A Java library to link QuPath with ImgLib2.

## Sample script

Here is a sample script that shows how to use the library from QuPath:

```groovy

import qupath.ext.imglib2.ImgBuilder

import qupath.ext.imglib2.ImgLib2ImageServer

import net.imglib2.type.numeric.ARGBType

var server = getCurrentServer()

// Create Img from level

var level = 0

var img = ImgBuilder.createBuilder(server).buildForLevel(level)

println img

// Create RandomAccessibleInterval from downsample

var downsample = 1

var randomAccessible = ImgBuilder.createBuilder(server).buildForDownsample(downsample)

println randomAccessible

// In previous examples, the type of the output image is not checked, which creates unchecked cast warnings

// (visible from Java, not Groovy). A better solution in Java to explicitely declare the output image type:

var type = new ARGBType()   // only valid if server represents a RGB image. Otherwise:

                            // net.imglib2.type.numeric.integer.UnsignedByteType for UINT8 images

                            // net.imglib2.type.numeric.integer.ByteType for INT8 images

                            // net.imglib2.type.numeric.integer.UnsignedShortType for UINT16 images

                            // net.imglib2.type.numeric.integer.ShortType for INT16 images

                            // net.imglib2.type.numeric.integer.UnsignedIntType for UINT32 images

                            // net.imglib2.type.numeric.integer.IntType for INT32 images

                            // net.imglib2.type.numeric.real.FloatType for FLOAT32 images

                            // net.imglib2.type.numeric.real.DoubleType for FLOAT64 images

var safeImg = ImgBuilder.createBuilder(server, type).buildForLevel(level)

println safeImg

// Once you have an image (or random accessible), you can use regular ImgLib2 functions

// For example, to read the pixel located at [x:1, y:2; c:0; z:0; t:0]:

var randomAccess = randomAccessible.randomAccess()

var position = new long[ImgBuilder.NUMBER_OF_AXES]

position[ImgBuilder.AXIS_X] = 1

position[ImgBuilder.AXIS_Y] = 2

var pixel = randomAccess.setPositionAndGet(position)

println pixel

// It is also possible to create an ImageServer from a RandomAccessible or Img

var newServer = ImgLib2ImageServer.builder(List.of(randomAccessible)).build()

println newServer

```