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BigStitcher Global optimization

555 bytes added, 14 January
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[[File:BigStitcher_optimize_simple1.png|center|600px]]
The options available here are:
 
* '''Do not find wrong links nor handle not connected tiles:''' run the global optimization once, taking all the links in the tile-network (that were not filtered out previously) into consideration. This is the fastest strategy, but it might lead to bad results if you have not carefully filtered out bad pairwise shifts or if there are multiple unconnected regions.
* '''Wrong link identification only:''' run the optimization iteratively, removing the worst link in the network until the average error of the tiles falls below certain thresholds (presets STRICT and RELAXED). This strategy is more robust against a few "bad" links, but will not move unconnected regions relative to each other.
* '''Identify wrong links and handle unconnected Tiles:''' first, run optimization with wrong link identification (with threshold presets STRICT and RELAXED) and then use shifts from metadata to align connected components relative to each other (while keeping the results from the first round within a component).
* '''Show full options dialog:''' Allow for the manual setting of thresholds in the next step.
This will immediately update the tile locations in the BigDataViewer, if it is open. If you want to un-do this step, you can click {{bc|Remove Transformation|Latest/Newest Transformation}} in the main menu.
In the first dialog, you will be asked for the optimization strategy to apply:
* '''Simple One-Round:''' run the global optimization once, taking all the same as '''Do not find wrong links in the tile-network nor handle not connected tiles:''' (that were not filtered out previouslysee above) into consideration. This is the fastest strategy, but it might lead to bad results if you have not carefully filtered out bad pairwise shifts or if there are multiple unconnected regions.* '''One-Round with iterative dropping of bad links:''' run the optimization iteratively, removing the worst same as '''Wrong link in the network until the average error of the tiles falls below certain thresholds identification only:''' (see belowabove). This strategy is more robust against a few "bad" links, but will not move unconnected regions relative to each other.* '''Two-Round using Metadata to align unconnected Tiles:''' first, run same as '''Two-Round using Metadata to align Identify wrong links and handle unconnected Tiles:''' and then use shifts from metadata to align connected components relative to each other (while keeping the results from the first round within a componentsee above).
{{Notice|The computational cost of the global optimization is relatively minor in comparison to the pairwise shift calculation. We therefore recommend to use the '''Two-Round using Metadata to align unconnected Tiles''' strategy (and do so by default in the Simple Mode).}}
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