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hardware:controller [2022/06/10 23:51]
Jon Daniels [Required software and instructions] 		hardware:controller [2024/02/16 17:54]
Jon Daniels [Firmware]
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 In general firmware updates add new functionality and fix bugs while retaining backwards compatibility, though on rare occasion backward compatibility is compromised.  If you are not using Micro-Manager, you should double-check with the vendor of the acquisition software before updating firmware.  If you are using Micro-Manager, you should generally download the latest nightly build whenever you update firmware.  Conversely, if you are having problems with a recent build of Micro-Manager make sure that the controller firmware is the latest. In general firmware updates add new functionality and fix bugs while retaining backwards compatibility, though on rare occasion backward compatibility is compromised.  If you are not using Micro-Manager, you should double-check with the vendor of the acquisition software before updating firmware.  If you are using Micro-Manager, you should generally download the latest nightly build whenever you update firmware.  Conversely, if you are having problems with a recent build of Micro-Manager make sure that the controller firmware is the latest.
  
 +** Warning: these instructions are for iSPIM and diSPIM only.  If you have another type of ASI light sheet microscope (e.g. oSPIM or single-objective light sheet) contact ASI for guidance and for the proper firmware files.  **
 ==== Before you begin ==== ==== Before you begin ====
  
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   * An alternative to deskewing is reslicing.  This can be as simple as reshuffling pixels in memory if the stage translation speed is chosen to be an integer number of pixels. Reslicing along the stage direction spreads the optical low-resolution between 2 axes but reduces the empty regions created by deskewing, particularly for long stage-scan stacks.  The following diagram hopefully helps:{{ :hardware:deskew_vs_reslice.jpg?600 |}}   * An alternative to deskewing is reslicing.  This can be as simple as reshuffling pixels in memory if the stage translation speed is chosen to be an integer number of pixels. Reslicing along the stage direction spreads the optical low-resolution between 2 axes but reduces the empty regions created by deskewing, particularly for long stage-scan stacks.  The following diagram hopefully helps:{{ :hardware:deskew_vs_reslice.jpg?600 |}}
   * It would be highly desirable for analysis and viewing software to be able to handle the deskew operation in memory and on the fly.  To date the only software known with this capability is FIJI's Big Data Viewer. Lobby your favorite software provider for this and make life better for everyone (many light sheet microscopes including lattice light sheet also require the same deskew step).   * It would be highly desirable for analysis and viewing software to be able to handle the deskew operation in memory and on the fly.  To date the only software known with this capability is FIJI's Big Data Viewer. Lobby your favorite software provider for this and make life better for everyone (many light sheet microscopes including lattice light sheet also require the same deskew step).
 +  * Micro-Manager 2.0 has a helpful ability to reslice data (an "Image Processor" added mid-2023) which is helpful especially for stage scanning data. The GPU version of the algorithm can operate on datasets up to 1/4 of the GPU memory, e.g. 2 GB datasets can be processed on a GPU with 8 GB of working memory.  The GPU version does interpolation and the CPU version is faster but doesn't do any interpolation.
 ==== Micro-Manager Implementation Notes ==== ==== Micro-Manager Implementation Notes ====
   * The spacing between slices is specified in the plugin, so the stage moves sqrt(2) times that distance per slice for 45 degree geometry (the actual angle can be set as of March 2018). There may be very small rounding errors (which would come out in normal post-processing) but the metadata should contain the actual slice spacing instead of the user-specified one.  Rounding errors were reduced as of the 2018-03-15 nightly build.   * The spacing between slices is specified in the plugin, so the stage moves sqrt(2) times that distance per slice for 45 degree geometry (the actual angle can be set as of March 2018). There may be very small rounding errors (which would come out in normal post-processing) but the metadata should contain the actual slice spacing instead of the user-specified one.  Rounding errors were reduced as of the 2018-03-15 nightly build.

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