Modification of Opera Sublayout - stoeter/Fiji-Tools-for-HCS GitHub Wiki

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Modification of Opera Sublayout

  • Setting up the order of acquired fields is essential for running the "Fish_Embryo_Screen" macro set.
  • If the order is wrong tiling of the macro Macro_Opera_Stack_Montage_for_Fish.ijm will be wrong

Opera Standard Sublayout File

  • Sublayouts can be created by right-click in the OperaDB and selection of sublayout
  • The Opera software EvoShell creates the .sly file that stores the positions within the well
  • The .sly file has a xml format and can be edited with a text editor (see example XML)
  • Opera starts counting fields in the middle and continues from top to bottom, left to right
  • Use any xml visualization (syntax high lighting) to inspect the structure
  • ATTENTION: Opera sublayout (as visulazed in the software) is 90° turned clock-wize. That means you need to turn what you see 90° turned counter clock-wize in order to know the really position!

Setting Sublayout for Opera

  1. Choose fields next to each other that later can be tiled later and save .sly on Opera
  2. Choose no overlap
  3. Open the .sly file and edit with text editor
  4. Special order is needed: from top left to bottom right within the well (ATTENTION: remember the 90° turning)
  5. Move the "Points" with their x an y values around so that they are in the right order (everything within the brackets)
  6. Save under new name and try it in a Opera acquisition
  7. Images should be now in the right order

Fine Tuning of Field Positions

  1. Try to tile the image with ImageJ/Fiji or run the Macro_Opera_Stack_Montage_for_Fish.ijm to see the tiling results
  2. If there is overlap of images or there are gaps after the tiling you need to change the positions in the .sly
  3. Most likely the y positions need to be adjusted
  4. Save under new name and check tiling again
  5. This is an iterative and empiric process to find the right positions/distances for the fields
  6. ATTENTION: if 2 channels or more are used make sure you run an entire exp file in EvoShell. If you use the manual mode there is no image correction. Running an experiment will also lead to scew correction and corrected images will have a smaller size
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