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docs:deskew [2024/05/20 16:32]
Jon Daniels created 		docs:deskew [2025/12/02 23:04] (current)
Jon Daniels [Related Resources]
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 You can reslice existing data that is open in Micro-Manager using the very bottom drop-down menu to select the dataset that you wish to use and then click the "Process" button. You can reslice existing data that is open in Micro-Manager using the very bottom drop-down menu to select the dataset that you wish to use and then click the "Process" button.
  
-Many of these functionalities will be integrated in the LightSheetManager plugin+Many of these functionalities will be integrated in the LightSheetManager plugin. 
 + 
 +Important: as of Nov 2024 the MM2.0 plugin uses a different convention than the MM1.4 datasets for the z_step parameter.  See https://github.com/micro-manager/micro-manager/issues/1984. 
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 +===== Related Resources ===== 
 + 
 +  * Jacob Lamb's paper referenced above has a python deskew implementation: https://doi.org/10.1364/BOE.479977 
 +  * Talley Lambert's LLSpy for lattice data includes deskew capabilities: https://github.com/tlambert03/LLSpy 
 +  * Volker Hilsenstein's lls_dd for lattice data includes deskew capabilities: https://github.com/VolkerH/Lattice_Lightsheet_Deskew_Deconv 
 +  * Talley Lambert's napari-ndtiff includes deskew capabilities: https://napari-hub.org/plugins/napari-ndtiffs.html 
 +  * Stephan Preibisch's BigDataViewer in FIJI includes the ability to specify affine transforms including to deskew, see an [[software:fiji_mvr|example script for diSPIM data]]
  
  
  

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