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magnify's Issues

Reader does not output helpful errors

Right now the entire Reader class will output unhelpful stack traces or even worse: will fail in a later part of the pipeline. We should output helpful messages instead to help users diagnose problems and fail fast by checking user inputs.

Bead finding fails for beads that are brighter at the edge.

Right now bead finding assumes that beads are high-intensity circles. But this isn't always the case: e.g. when imaging in brightfield or when things are bound to the surface of the bead.

We should make it so both types of bead can be found. Ideally this would happen automatically without the user needing to specify a bead finding method.

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