Overlaying

Author

Kaitlin Sullivan

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Video Tutorial

Here we will make opaque overlays to circumvent Merge Channels...ā€™s 7-channel limit as well as the avoiding additively combining colours.

HiPlex Overlay

This option creates a representative overlay image of your binarized gene expression images.

  1. Download the .lut files from here
  2. Place them in the FIJI lut folder
  3. Re-start Fiji

TO RUN: - Drag-and-drop your first gene image from the overlay folder into FIJI and select HiPlex Overlay from the menu

WHAT HAPPENS:
- When running, images will be opaquely overlaid and the order and colours of the images will print out in the Log box.

OUTPUT:
- The image will save in the overlay folder as TestCOMP.png.

DRAWBACKS AND WORKAROUNDS In the future, there will be a plug-in option to change the colours and order of overlay images
- Right now this only allows up to 12 colours without any control over their order or assigned colour. - To create a manual overlay image: pseudocolour according to prefered image colours and and use FIJIā€™s Image -> Overlay... -> Add Image with zero background checked!

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