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ImageJ2 and BigDataViewer and ... #66

dietzc opened this issue Mar 1, 2017 · 0 comments

ImageJ2 and BigDataViewer and ... #66

dietzc opened this issue Mar 1, 2017 · 0 comments


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@dietzc dietzc commented Mar 1, 2017

After a discussion with @ctrueden in person, we found that it might make sense to open an issue to discuss what steps would be required on ImageJ2 side to allow the following relatively simple use-case using ImageJ2 + BigDataViewer:

Region of Interests in BigDataViewer (2D) with very large images

Use Cases

Display of Segmentation Results

Allow display ImgLabelings alone or on top of other images.

Manual Annotation

Allow to manually draw region of interests (Polygon, Rectangle, Freehand,...) in BigDataViewer.


For each annotation we want to measure features of the roi and output the result in a Table


We want to be able to process only the selected regions of interests. If the output is some RAI again only the updated regions should be updated in the BDV.

What's missing?

  1. BigDataViewer in 2D mode
  2. Allow manual creation of ROIs in BigDataViewer 2D mode.
  3. Allow ImageJ2-Commands to consume these ROI information.
  4. Allow ImageJ2-Commands to update the entire image or only the processed pixels in the
    displayed image.

All of this is somehow related to RichImg, imglib2-roi and SCIFIOImgPlus. However, a lot of this functionality is already in place (Cache, CellImg,, partial update of images in BDV etc). However, some projects have to be finished first and the final functionality has to be made available in ImageJ2-Command developers in an easy manner, especially the BigDataViewer API.

Please feel free to add (simple) use-cases, comments etc as needed.

@fjug @tpietzsch

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