Commit d198b1f6 authored by Martin Schorb's avatar Martin Schorb
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docs usage, export

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......@@ -138,3 +138,30 @@ You will see a 3D graph containing all the tiles and their interconnections. The
-**Select Transform type:** Select a transformation type to be used for the solving. `rigid` or `TranslationModel` should match for most volume EM data (except ssTEM).
-**Select solve type:** You can choose between `2D` (inside one section only) and `3D` considering the full volume for the solve.
### Export Render stack to volume
You can export a Render stack at any time to disk ("materialize").
![export](img/webui_export_slice.png "VolumeAlign WebUI export")
You can **explore slice** to determine the **volume region to consider**.
At the moment only `N5` is available as **output type**.
Pick the desired **output path** and the result will appear in a sub-directory `aligned` with the date and a reference to the stack.
With the known number of tiles and the estimated run time for exporting a tile, the necessary compute resources for the stack are predicted and can be checked in **Compute settings**.
![export](img/webui_export_computesettings.png "VolumeAlign WebUI export")
Launching the computation will request the selected resources on the cluster and then launch a Spark instance on the allocated compute nodes that distributes and manages the parallel computation of the point matches.
You will receive an email once the computation is done. It will tell you that the computation was `CANCELLED` but this only means that the resource allocation has been ended after successful computation of the matches. If you get a message referring to a `TIMEOUT`, you have to re-run the computation with more generous resource settings.
## Finalize output format
Here you can finalize your data export and generate the necessary metadata file to view the volume in BigDataViewer or MoBIE.
Currently only `BDV-XML` is supported as **post-processing target format**.
- **Choose exported volume:** This provides a list of already exported volumes. The files have to still reside in the original location on the storage system.
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