Zeiss AxioZoom microscope
Skirball 4th floor

Protocol for opening 96 Well Plates and Montaging in ImageJ

This requires 2X memory available to ImageJ to open all 96 wells.

Edit > Options > Memory& Threads... to add more memory.

• Plugins > Macros > Install 96wellplatesmacros.txt.
• Close all open images in ImageJ.
• Open the .czi file into ImageJ.
  Sometimes you may drag and drop and it will open automatically.
  Otherwise, use the LOCI plugins from the Plugins tab.
  Plugins > LOCI or Plugins > Bio-Formats
• Select Hyperstack as per below image:
  
• Select All series and then OK as per below:
  
• 96 images should open.
• Plugins > Macros > .czi 96 wells to stack & montage
• At the end you should have three new files in the same folder at the original dataset:
  1. Raw data in Tiff format.
  2. RGB version with your contrast enhancement.
  3. A montage.
   

first posted 20150223_1353; last updated 20150528_1140

Michael.Cammer@med.nyu.edu or mcammer@gmail.com