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docs:mm_dispim_plugin_user_guide [2019/07/03 00:03]
Jon Daniels [Acquisition Mode]
docs:mm_dispim_plugin_user_guide [2019/10/26 00:07] (current)
Jon Daniels [Data Analysis Tab]
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 Based on the angle specified on the settings tab "Path A stage/​objective angle",​ the pixel size defined in Micro-Manager’s “Pixel Size Calibration”,​ and slice spacing then the plugin runs the deskew. ​ If empirically it is off, check the "​Invert direction"​ checkbox and try again. ​ Deskew fudge factor is an additional scale factor on the deskew and should generally be 1. Based on the angle specified on the settings tab "Path A stage/​objective angle",​ the pixel size defined in Micro-Manager’s “Pixel Size Calibration”,​ and slice spacing then the plugin runs the deskew. ​ If empirically it is off, check the "​Invert direction"​ checkbox and try again. ​ Deskew fudge factor is an additional scale factor on the deskew and should generally be 1.
  
 +
 +===== Synthetic Stage =====
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 +Sometimes it is handy to create a synthetic stage to move the sample relative to the optic axis, e.g. to move deeper into the sample along the imaging axis by moving the SPIM head and the X axis of the XY stage together. ​ In the hardware config wizard add an instance of the Utilities > Multi Stage device which creates a synthetic 1D stage out of 2 real 1D stages. ​ Specify which stages to use and the scale factors in the properties in the System-Startup group in your hardware config. ​ The scale factors should be +/- 1 for 45 degrees, +/- 1 and +/- 2 for oSPIM at 60 degrees, and so forth.
 +
 +In order to use one axis of an XY stage as a 1D stage for the Multi Stage device you can use the Utilities > Single Axis Stage device. ​ Set its properties in the System-Startup group as well.
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 +Once set up, it is likely best to use the new Multi Stage device via the Stage Control plugin rather than assigning it as a stage in the Micro-Manager plugin.