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Fiji built from source has discrepancies with the Fiji user distribution #39
This issue describes a blanket problem that we may want to file into separate issues on a per-artifact basis. There will always be some discrepancies between what is built from source (i.e., the latest master branch) and what has been uploaded to the updater (i.e., the latest tested-and-working binaries). This is a good thing.
However, at the time of this writing, there are actually many discrepancies that cannot be explained by differences in the Fiji source code itself.