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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 [2020/04/28 19:41]
Jon Daniels [Default Timing] |
| ==== Default Timing ==== | ==== Default Timing ==== |
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| Specify the **Sample exposure [ms]** in Slice Settings, and either define the slice period or let the plugin minimize the slice period automatically. The timing depends on the reset and readout time of the cameras; plugin code specific to each supported camera computes timings for the user-specified ROI using information provided by the manufacturer (usually either via their detailed camera documentation or read-only Micro-Manager properties). Any extra time in the slice is placed before the camera trigger to allow maximum time for piezo settling. The values computed by the default timing mode are shown in the slice timing settings and can be subsequently modified manually. | Specify the **Sample exposure [ms]** in Slice Settings, and either define the slice period or let the plugin minimize the slice period automatically. The timing depends on the reset and readout time of the cameras as well as the trigger mode set on the [[docs:mm_dispim_plugin_user_guide#cameras_tab|Cameras tab]] (e.g. "Overlap/synchronous" trigger mode performs readout and reset at the same time whereas they are sequential in "Edge" mode). Plugin code specific to each supported camera computes timings for the user-specified ROI using information provided by the manufacturer (usually either via their detailed camera documentation or read-only Micro-Manager properties). Any extra time in the slice is placed before the camera trigger to allow maximum time for piezo settling. The values computed by the default timing mode are shown in the slice timing settings and can be subsequently modified manually. |
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| <WRAP center round tip 60%> | <WRAP center round tip 60%> |
| 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. |
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| | ===== 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. |
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| | 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. |
