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Add (interactive) background correction #197
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This reverts commit 53f9e8d. The commit used ImageJ2 which clashes with some of the other dependencies in the project.
Otherwise, the webserver complains about the request for tile specs being too large
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This PR adds tools for correcting global shading on large FIBSEM volumes (e.g., here). These tools are:
For supplying model parameters to the spark client, I used an ad hoc json representation, since the model is expected to vary in z. This representation is documented in
BackgroundCorrectionClient
. Feedback about the documentation and the representation itself is very welcome.One particular problem with doing this at the level of a stack is that we would need an exported mask to not also correct regions where there is no tissue. Is it safe to assume that a mask will always be exported when background correction is done? In this case, I will add support for masks.