[WIP] Draft: Add ability to select series with java backend, giving access to macro, label, and sub resolution images

[NHPatterson]

This is a start to selecting a series index within the image in using the bioformats backend #11 . Consider this a draft to start a dialogue on how you'd like to best to do (if interested at all).

This very simple version does access other images in the file, but as the OME metadata seems to be driving all the metadata information, sometimes things get replicated. I.e,. the macro image in a Zeiss .czi file reports the pixel resolution of the base microscopy image rather. This seems to be case-by-case. Other images report nothing at all for physical size because sub-resolutions aren't necessarily mapped by OME metadata. Obviously these could be resolved from the dimensions if one were to sweep all the series.

This is all I did:

1. Add argument to select series_idx to base classes.
2. Use series index to extract appropriate metadata for that series.
3. Pass argument to java reader.

[Nicholas-Schaub]

Hey, sorry for the delayed response.

One of the things we have discussed (but not started working on) is accessing pyramid/series data. The primary focus up to this point has really been on ease of use and performance, so a number of things have fallen by the wayside. However, we are in the process of dedicating people directly to fleshing out things like this. Pyramids are likely one of the first things we are going to tackle since we have an image visualization tool that directly reads image pyramids in ome tiff and ome zarr.

I'll take a closer look at this, do some thinking on the best way to do a full and integrated implementation (which you may have already accomplished), and get back to you soon. This is definitely something we need to implement, since we use bfio as our main platform ingestion tool and not being able to extract all series data is a known deficit of the current code.