Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
See https://github.com/idr-contrib/community/issues/5 and https://github.com/openmicroscopy/bioformats/pull/3083
The custom ScanrReader handling of missing planes that were implemented for the secretion study were lost when IDR Bio-Formats was upgraded to 5.4.x.
This should restore the two necessary commits to handle missing files as black planes.