Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
docs:mm_dispim_plugin_user_guide [2024/05/04 00:14]
Jon Daniels [Data Analysis Tab] 		docs:mm_dispim_plugin_user_guide [2024/10/05 13:57] (current)
Jon Daniels [Save and Load]
Line 319: Line 319:
 In the future we would like to include the ability to manipulate the acquired data, including registration of the two views and joint deconvolution, directly in the diSPIM plugin. At present, the Data analysis tab, (<imgref plugin_DataAnalysis>), exports the acquired data to the format required by the MIPAV GenerateFusion plugin. Fiji’s Multiview Registration plugin can directly import diSPIM data. Exporting operates on the top-most image window. In the future we would like to include the ability to manipulate the acquired data, including registration of the two views and joint deconvolution, directly in the diSPIM plugin. At present, the Data analysis tab, (<imgref plugin_DataAnalysis>), exports the acquired data to the format required by the MIPAV GenerateFusion plugin. Fiji’s Multiview Registration plugin can directly import diSPIM data. Exporting operates on the top-most image window.
  
-<imgcaption plugin_DataAnalysis| The Data Analysis panel facilitates exporting acquisition data.>{{:docs:um-datatab.png?600| diSPIM plugin Data Analysis tab}}</imgcaption>+<imgcaption plugin_DataAnalysis| The Data Analysis panel facilitates exporting acquisition data.>{{:docs:um-dataanalyis-tab.png?600| diSPIM plugin Data Analysis tab}}</imgcaption>
  
 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.  Rotate direction should be enabled if the data moves up/down in the raw data while scrolling through instead of left/right. 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.  Rotate direction should be enabled if the data moves up/down in the raw data while scrolling through instead of left/right.
Line 395: Line 395:
  
 **Load Playlist:** Load a json file into the acquisition playlist, populating the acquisition table and position lists. **Load Playlist:** Load a json file into the acquisition playlist, populating the acquisition table and position lists.
 +
 +===== Plugin Settings =====
 +
 +The plugin settings are stored in the windows registry adjacent to other Micro-Manager settings at Computer\HKEY_CURRENT_USER\SOFTWARE\JavaSoft\Prefs\org\micromanager\asidispim.

Trace: