BUG: ZeissCZIReader (seriesMetadata is empty)

[bramalingam]

ref: ​https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8119

BF Version : 5.2.1

Testing summary:

Tried opening the file on Fiji,
and each tile was referred by a series #.
So tried to extract the seriesMetadata() using Matlab for each tile.

Tried the following Matlab code,

clear all;close all;

reader = bfGetReader('/Users/bramalingam/Desktop/QA17333/Slide02_10x_RGT_Shading Correction.czi');
omeMeta = reader.getMetadataStore();
seriesMetadata = reader.getSeriesMetadata();
globalMetadata = reader.getGlobalMetadata();

%Print out all timestamps in seriesMetadata
keys = seriesMetadata.keys;
for i=1:seriesMetadata.size()

key = keys.nextElement();
value = seriesMetadata.get(key);
fprintf('%s = %s\n', key, value)

end

But the seriesMetadata is empty. So the 'scene'/'position' information needs to be populated for each series(as requested by the user).

[bramalingam]

​https://github.com/openmicroscopy/bioformats/pull/2600

[bramalingam]

The overlap percentage can be calculated by comparing the X,Y positions and the size of the tile between consecutive frames, by the user. Thus not adding that method to the reader.