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software:imagej_macro [2016/02/10 17:48]
Abhishek Kumar created 		software:imagej_macro [2019/08/08 20:56] (current)
Melissa Glidewell Noted that macro is now deprecated; add link to new macro
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 ====== Imagej Macro  ====== ====== Imagej Macro  ======
  
-Min Guo and Hari Shroff, February 2016+***Deprecated: Please see [[software:GPU_diSPIMFusion|diSPIM Preprocessing]]*** 
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 +Min Guo, Yicong Wu, and Hari Shroff, February 2016
  
 Tutorial for using the image shifting macro, for diSPIM data acquired in stage-scanning mode Tutorial for using the image shifting macro, for diSPIM data acquired in stage-scanning mode
  
-The image shifting macro preprocesses diSPIM data acquired in stage-scanning mode before further analysis (e.g. deconvolution, segmentation etc.). The macro offers background subtraction, image shifting and automated region of interest detection in a graphical user interface for easy user interaction and review. +The image shifting macro {{:software:imagei_macro.zip|}} preprocesses diSPIM data acquired in stage-scanning mode before further analysis (e.g. deconvolution, segmentation etc.). The macro offers background subtraction, image shifting and automated region of interest detection in a graphical user interface for easy user interaction and review. 
 The macro enables users to process both single-view (iSPIM) images and dual-view (diSPIM) images.  Its main task is to transform the stage-scanning coordinate system into the more conventional coordinate system (stage stationary, light-sheet and detection plane swept through sample). In stage-scanning mode, the diSPIM moves the stage (and sample) at constant speed, but keeps the light sheet and detection objective stationary. The relative movement between the sample and detection lens leads to the following relationship between the two coordinate systems: The macro enables users to process both single-view (iSPIM) images and dual-view (diSPIM) images.  Its main task is to transform the stage-scanning coordinate system into the more conventional coordinate system (stage stationary, light-sheet and detection plane swept through sample). In stage-scanning mode, the diSPIM moves the stage (and sample) at constant speed, but keeps the light sheet and detection objective stationary. The relative movement between the sample and detection lens leads to the following relationship between the two coordinate systems:
      

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