Hi Oli,
This new behavior is a bit troublesome as now we have duplication of the image series for the same data. Are there always a fixed number of images in the pyramid or is this dependent on other factors?
The number of resolution levels in the pyramid is generally dependent upon the size of the highest resolution.
Also, asides from the first (max res) and last (lowest res) images, the intermediate resolution images are cropped/clipped, the missing pixels showing as black.
If you would like, I can send you a dataset showing this.
We'd be happy to look into this if you can send an example. As usual,
http://qa.openmicroscopy.org.uk/qa/upload is the best place to upload, but if you are uploading more than 2 GB of data let me know and I will send FTP instructions privately.
A better aproach, at least for us, was something that a previous version of BioFormats was doing. Adding the intermediate resolutions as separate slices or timepoints that we could manipulate by using crop on import. Though the fact that they are all the same (largest) size is not optimal, I can imagine.
We stopped using that approach because it quickly gets out of hand when there are also multiple Z sections and/or timepoints. The current approach is, from a modelling standpoint, much more correct. The Bio-Formats Java API allows for distinguishing between a series that is part of a pyramid and a series that is just extra data (see
http://downloads.openmicroscopy.org/bio ... tionCount()); this just hasn't been mirrored in the macro language commands yet. It is our intention to do that no later than the 5.1.0 release.
Regards,
-Melissa