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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 [2025/05/20 17:18] (current)
Jon Daniels [Overview Acquisition] |
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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. |
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| 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: |
| ==== Overview Acquisition ==== | ==== Overview Acquisition ==== |
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| As of March 2019 there is a feature to acquire an overview acquisition. This is useful when the entire sample is many times larger than the instantaneous field of view. The overview image is a 2D image representing a thin slice of the sample which can be collected relatively quickly. After acquisition, a rectangle is placed on the overview image representing the current stage position, and this rectangle moves with the stage as long as positions are being updated. It is not intended for use with a Z grid but only XY grid. | The overview acquisition is useful to orient the user in the context of the larger sample when it is many times larger than the instantaneous field of view of the microscope. It creates relatievly quickly a 2D overview image representing a thin slice of the sample. After the overview acquisition runs the overview image is displayed. A rectangle overlay is placed on the overview image representing the current stage position, which rectangle moves with the stage as long as positions are being updated. |
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| Some settings for the overview acquisition reside on the "Data Analysis" tab. These include the downsample factor for XY and for slice spacing. The fractional thickness specifies how much of the entire image will be max projected to form the overview image. You specify a channel and a side to run the overview acquisition with. | Overview acquisitions are intended for use with an XY grid only, not a Z grid. Running the overview acquisition uses the current settings of the XYZ grid GUI for X and Y (if they are enabled) and will overwrite any existing position list. |
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| Running the overview acquisition with the thus-labeled button uses the current settings of the XYZ grid GUI for X and Y (if they are enabled) and will overwrite any existing position list. | Some settings for the overview acquisition reside on the “Data Analysis” tab. These include the downsample factor for XY and for slice spacing. The fractional thickness specifies how much of the entire image will be max projected to form the overview image. You specify a channel and a side to run the overview acquisition with. |
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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. |
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| <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> |
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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. 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. |
