ImgLib2 Resources

General ImgLib2 Resources

• Blog: https://imglib.github.io/imglib2-blog/
• GitHub Repository: https://github.com/imglib/imglib2
• ImageJ Documentation: https://imagej.net/imglib2/

Video Lectures

• Albert Cardona - Fast scripting with ImgLib2 in Fiji’s Script Editor
  • Video: Watch here
• Stephan Saalfeld - Large data lazy processing with ImgLib2 and CLIJ2
  • Video: Watch here

Tutorials and Notebooks

• Blog example on Jupyter Notebook: How to Display ImgLib2 Data
• (LOCI?) ImageJ Tutorials Jupyter Notebook1: ImgLib2 Basics
• (LOCI?) ImageJ Tutorials Jupyter Notebook2: ImgLib2 in Detail
• ImgLib2-intro : ImgLib2 introductory workshop (older)
• ImgLib2-advanced : ImgLib2 advanced workshop (older)
• Saalfeldlab ImgLib2-intro I2K2020 ImgLib2 Intro
• Saalfeldlab ImgLib2-advanced : I2K2020 ImgLib2 Advanced
• Saalfeldlab i2k-tutorial: I2K2020 tutorial (Use N5, ImgLib2-Cache, and Spark)
• DAIS learnathon by Matthias Arzt: imglib2-algorithm-workshop
• DAIS learnathon by Tobias Pietzsch: imglib2-cache-examples

Learning ImgLib2 discussions at image.sc

• Learning ImgLib2 Development
• Other threads on Image.sc
• ImgLib2 Documentation on imagej.net wiki

References

• Publication : Tobias Pietzsch, Stephan Preibisch, Pavel Tomančák, Stephan Saalfeld, ImgLib2—generic image processing in Java, Bioinformatics, Volume 28, Issue 22, November 2012, Pages 3009–3011, https://doi.org/10.1093/bioinformatics/bts543
• See also BigDataViewer Resources

Uncategorized

• nta.kt (Saalfeld lab) The nta.kt library brings n-dimensional transformation and algebra to Kotlin. It combines the expressive power and flexibility of the Java image processing library ImgLib2 with the convenience and clarity that Kotlin language features provide.
• imglib2-trainable-segmentation (random forests) (Matthias Arzt, DAIS project) The repository shows example programs for segmentation of 2D and 3D images using random forests. One only needs to provide an input image and its (segmentation) labeling.