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Imaging refactor part 2 - Atoms: add_atoms(), refine_atoms(), plot(kind='atoms') and tests - #236

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Imaging refactor part 2 - Atoms: add_atoms(), refine_atoms(), plot(kind='atoms') and tests#236
darshan-mali wants to merge 14 commits into
electronmicroscopy:devfrom
darshan-mali:imaging_refactor

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