Writing in front: (A)
- Make sure your MATLAB Version is not lower than R2021b.
- (Optional) You can install python with package: tifffile and numpy, on your local machine for fast IO support when processing tiff file
- (Optional) For advanced user, you can change the threads number per worker by configurating Reg3D_local.mlsettings or Reg3D_server.mlsettings. Because of the 'hyper-thread' technology, you can get fully performance.
(B) (Optional) You can install VC_redist.x64.exe for fast nd2 file loading, read README in \extern\microsoft support for more detail.
[Two Channels Registration Pipeline]
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select the template as fix frame, for better performance, we recommand you select the local stable best
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using 'translate' as transformation for object location estimating
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set the initial iteration step bigger than default(6.25e-2), which could be choosed from 0.1 to 0.15
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set the iteration factor bigger than default(0.5), which could be choosed from 0.6 to 0.8
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set the robustness factor bigger than default(0.5), which could be choosed from 0.6 to 0.9
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check the 'Enable' checkbox to confirm registration(global) setting
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make sure you are working on source 'raw', and click the 'Run' button Until the app is stopped, you can go to next step#
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if 'translate' is not accurate enough, and the object has some rotation motion or stretch motion, using 'rotation' or 'similarity' as transformation
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you may decrease the minimal iteration step for good accuracy, such as 1e-6 or smaller, where 1e-5 as default
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set the initial iteration step as default(6.25e-2) or smaller
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set the iteration factor as default(0.5) or smaller
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set the robustness factor smaller than default(0.5), which could be choosed from 0.01 to 0.2
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you can crop the image in XY plane for better registration speed
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make sure you are working on source 'registrated', and click the 'Run' button Until the app is stopped, you can go to next step# [Warning] Do not run on 'registrated' too many times(more than 3 times), because of interpolation may decrease the spatial and temporal resolution.
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if there is also some local motion, you can choose registration(local) setting panel, using the template which came from 'global' is better
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modify the cumulative field smooth value, the value is smaller, the local motion registration is stronger
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you can skip this step, if marker channel with low photobleaching, or you can check the 'compensate photobleaching' checkbox for better performance
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check the 'Enable' checkbox to confirm registration(local) setting
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make sure you are working on source 'registrated', and click the 'Run' button Until the app is stopped, you can go to next step#
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if there are some bad registration frames, you can cut them or use registration(manual) for manual resiatration
[One Channel Registration Pipeline]
- same as two channel but functional channel is also the structured channel
[Longterm Registration Pipeline] 1.
Go and have fun!
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