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docs:mm_dispim_plugin_user_guide [2024/02/21 21:16]
Jon Daniels [Cameras Tab] 		docs:mm_dispim_plugin_user_guide [2024/10/05 13:57] (current)
Jon Daniels [Save and Load]
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 If you are not familiar with Micro-Manager, please read the [[https://micro-manager.org/wiki/Micro-Manager_User%27s_Guide|User Guide]] and [[https://micro-manager.org/wiki/Micro-Manager_Configuration_Guide|Configuration Guide]] before running the plugin. Also, refer to the diSPIM manual: Getting started with Micro-Manager for guidance before aligning your diSPIM. If you are not familiar with Micro-Manager, please read the [[https://micro-manager.org/wiki/Micro-Manager_User%27s_Guide|User Guide]] and [[https://micro-manager.org/wiki/Micro-Manager_Configuration_Guide|Configuration Guide]] before running the plugin. Also, refer to the diSPIM manual: Getting started with Micro-Manager for guidance before aligning your diSPIM.
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 +Currently the diSPIM plugin is supported in 1.4.x only.  In 2023 there have been efforts to create a new plugin in Micro-Manager 2.0 called [[https://github.com/micro-manager/LightSheetManager|LightSheetManager]] that will operate the diSPIM as well as other types of light sheet microscopes.  Contributions to the effort of making this new plugin are appreciated.  As of August 2023 this is in alpha testing by the first few bleeding edge adopters, and we expect that by end of 2023 it will be ready for more adopters and a full replacement in 2024.
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 +You can download the nightly builds of Micro-manager 1.4 for Windows [[https://download.micro-manager.org/nightly/1.4/Windows/|here]]; the date is encoded in the file name and the latest date is at the top of the page.  Make sure to get the appropriate 32bit or 64bit depending on your computer.
  
 Before running the diSPIM plugin, create or load a Micro-Manager hardware configuration with all the relevant devices. The plugin is accessed through the Micro-Manager menu bar: **Plugins > Device Control > ASI diSPIM**. The plugin has 10 tabbed panels for different features and tasks. After opening the plugin, first configure the Devices Tab. Keep the main Micro-Manager window accessible; the plugin generally does not duplicate functionality already provided there. In addition to the tabbed panels, a sidebar provides a color coded “quick glance” indication of each axis’ position: Before running the diSPIM plugin, create or load a Micro-Manager hardware configuration with all the relevant devices. The plugin is accessed through the Micro-Manager menu bar: **Plugins > Device Control > ASI diSPIM**. The plugin has 10 tabbed panels for different features and tasks. After opening the plugin, first configure the Devices Tab. Keep the main Micro-Manager window accessible; the plugin generally does not duplicate functionality already provided there. In addition to the tabbed panels, a sidebar provides a color coded “quick glance” indication of each axis’ position:
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 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.+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.
  
  
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 **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.
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 +===== Plugin Settings =====
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 +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.

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