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docs:mm_dispim_plugin_user_guide [2023/06/09 13:34]
Jon Daniels [Cameras Tab] 		docs:mm_dispim_plugin_user_guide [2024/04/15 23:19]
Jon Daniels [Micro-Manager diSPIM Plugin User Guide]
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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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 <imgcaption plugin_Cameras| The Cameras panel allows you to set the ROI and the acquisition trigger mode.>{{:docs:um-camerastab.png?600| diSPIM plugin Cameras tab}}</imgcaption> <imgcaption plugin_Cameras| The Cameras panel allows you to set the ROI and the acquisition trigger mode.>{{:docs:um-camerastab.png?600| diSPIM plugin Cameras tab}}</imgcaption>
  
 +==== Simultaneous Cameras ====
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 +This option was added so that multiple cameras could be used on the same path, e.g. a single-view SPIM with 4 different cameras to record each camera looking at a different spectral window at the same time.
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 +Due to Micro-Manager viewer limitations there are some oddities about this feature's implementation.  In simple cases with only 2 cameras it may be easier to instead use the setting on the Settings tab to record from 2 views simultaneously.  When using "Use simultaneous cameras on Path A" each "channel" in the dataset is a different camera as expected.  However if multiple channels are used also, each channel is assigned a portion of the resulting stack, and furthermore no time points are allowed.  For instance with 2 cameras and 3 sets of lasers and 50 slices in the stack the resulting dataset would have 2 channels and 150 slices.
 ===== Settings Tab ===== ===== Settings Tab =====
  
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 The scanner (micromirror) drive card has adjustable Bessel output filters to protect the filter from being driven near its mechanical resonance (usually 2 kHz). Settings as high as 0.8 kHz are usually acceptable, and in general the shorter the scan period (and faster frame rates) the more this matters. The scanner (micromirror) drive card has adjustable Bessel output filters to protect the filter from being driven near its mechanical resonance (usually 2 kHz). Settings as high as 0.8 kHz are usually acceptable, and in general the shorter the scan period (and faster frame rates) the more this matters.
  
 +==== Simultaneously acquire from both paths/cameras ====
 +
 +This option was added to enable reflective imaging where cameras on both sides are triggered together (see https://www.nature.com/articles/s41467-017-01250-8).  Both cameras should be wired to the same trigger signal using e.g. a BNC "tee" at the Tiger controller output.
  
 +Note this is similar but distinct from the option to acquire multiple cameras on Path A which is configured on the Cameras tab.  However in many cases either one can functionally be used.
 ===== Acquisition Tab ===== ===== Acquisition Tab =====
  

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