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At first glance, my hypothesis of what is the reason for the behavior you described is a "missing feature" (in libCZI) which goes under the name "mask support" (also listed here). If the document contains several scenes, and if the scenes are overlapping, then a multi-scene-composition may have artifacts like the ones you described. Rendering single scenes should work as expected, but not scene-compositions.
Please see also here. I regret, the situation hasn't changed since then.
@ptahmose thanks for the reply.
There must be some way to solve this issue, because if you refre Snapshot from ZEN viewer, it is getting correctly render for multi-scene-composition.
Please refer issue created on old git repo
zeiss-microscopy/libCZI#63 (comment)
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