Add extractor for BioFormats (CXD)

[weiglszonja]

Classes added:

• BioFormatsImagingExtractor: a base imaging extractor for files supported by BioFormats (supported formats)
• CxdImagingExtractor: a specialised imaging extractor for reading data and metadata from CXD files produced via Hamamatsu Photonics (HCImage Live software: https://hcimage.com)

Note:

To use these extractors bioformats_jar has to be installed with conda as: conda install -c conda-forge bioformats_jar. Additionally, the reader requires the java executable to be available on the path (or via the JAVA_HOME environment variable), if not found it has to be set as:

mac and linux: export JAVA_HOME=$CONDA_PREFIX

windows: set JAVA_HOME=%CONDA_PREFIX%\\Library

TODO:

• [x] need an example .cxd data from Howe lab
• [x] need to add unittests
• [ ] need to add conda install -c conda-forge bioformats_jar dependency for the CI tests

[pauladkisson]

FYI, Now that we have working API docs, this PR will need to add the new imaging extractors to list of imaging extractors in the api docs.

[weiglszonja]

Created PR for uploading the example file shared by the Howe lab: https://gin.g-node.org/CatalystNeuro/ophys_testing_data/pulls/22