Merge pull request #406 from rleigh-dundee/zvi-roi

ZVI: Parse ROIs correctly
merge dev_4_4 -D org -I include -E exclude: PR 379 (Fix source code links moved to the scifio-tools foder)
merge dev_4_4 -D org -I include -E exclude: PR 405 (Zeiss ZVI: use coordinates to retrieve the correct plane (rebased onto dev_4_4))