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docs:mm_dispim_plugin_user_guide [2019/05/30 09:12]
Jon Daniels [Acquisition Mode] |
docs:mm_dispim_plugin_user_guide [2019/10/26 00:07]
Jon Daniels [Data Analysis Tab] |
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| Currently several modes are supported: | Currently several modes are supported: |
| * Synchronous piezo/slice scan: standard use, the piezo and sheet move together through the sample | * Synchronous piezo/slice scan: standard piezo use, the piezo and sheet move together through the sample |
| * No scan (fixed sheet): neither the piezo nor light sheet moves; useful for characterizing vibration in the system | * No scan (fixed sheet): none of the piezo nor light sheet nor the stage moves (only the light sheet generation using the sheet axis); useful for characterizing vibration in the system |
| * Stage scan: uses the XY stage to move the sample through a fixed light sheet; for two-sided acquisitions, one view is collected in the first pass, and the second view is collected as the stage moves “back” for a second pass; see the document on stage scanning for details and requirements | * Stage scan: uses the XY stage to move the sample through a fixed light sheet; for two-sided acquisitions, one view is collected in the first pass, and the second view is collected as the stage moves “back” for a second pass; see the document on stage scanning for details and requirements |
| * Stage scan interleaved: same as stage scan except that the stage moves half as fast and the two light paths alternate, meaning both views are collected in the same pass; use caution if you are using a galvo to switch the laser between the sides, this can overstress some galvos | * Stage scan interleaved: same as stage scan except that the stage moves half as fast and the two light paths alternate, meaning both views are collected in the same pass; use caution if you are using a galvo to switch the laser between the sides, this can overstress some galvos |
| * Stage scan unidirectional: same as stage scan except the second view is taken while scanning in the same direction as the first view with a rewind step between. For 1-sided acquisitions stage scan and stage scan unidirectional are equivalent. For 2-sided acquisitions the stage scan unidirectional will take slightly longer (the rewind step is done at 75% of the max stage speed) but makes data processing easier. | * Stage scan unidirectional: same as stage scan except the second view is taken while scanning in the same direction as the first view with a rewind step between. For 1-sided acquisitions stage scan and stage scan unidirectional are equivalent. For 2-sided acquisitions the stage scan unidirectional will take slightly longer (the rewind step is done at 75% of the max stage speed) but makes data processing easier. |
| * Slice scan only: suppresses movement of piezo but moves the light sheet; useful for characterizing light sheet thickness | * Slice scan only: suppresses movement of piezo but moves the light sheet; useful for characterizing light sheet thickness and for autofocus |
| * Piezo scan only: the light sheet stays stationary but the piezo moves; useful for establishing axial PSF | * Piezo scan only: the light sheet stays stationary but the piezo moves; useful for establishing axial PSF and for autofocus |
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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. |
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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. |
