integration of more relevant metadata in read_metadata parse_metadata=True

[machth]

Description of feature

Feature integration in read_metadata(img_path, image_type="czi", parse_metadata=True)

1. extract scene information from czi file. (e.g. 'scene': [0,1,2,3] or 'scene': (0, 4))
2. extract exposure time and intensity (e.g. 'exposure time': [50, 100, ...] (in ms); 'intensity': [50,100,100, ...] (in %))

Optional:
3. If possible also extract dimensions of czi or each scene.
4. Extract dye information for better knowledge -> 'Fluor' in metadata

Example for 3.:
'dimensions': [{'X': (0, 2236), 'Y': (0, 2236), 'Z': (0, 1), 'C': (0, 6), 'M': (0, 42), 'S': (0, 1), 'H': (0, 1)}]
'shape_info': HSCZMYX
or
'shape_info': HSCZMYX
'shape': (1, 1, 6, 1, 42, 2236, 2236)

Example for 4.:
'dye': ['TL Brightfield', 'Alexa Fluor 633', 'Alexa Fluor 555', 'Alexa Fluor 488', 'DAPI', 'Cy7']

e.g. metadata (extracted information in bold)
'Dimensions': {'Channels': {'Channel': [
{'@id': 'Channel:1',
'@name': 'AF633',
'ExcitationWavelength': '631',
'EmissionWavelength': '647',
'DyeId': 'McNamara-Boswell-0055',
'DyeDatabaseId': '66071726-cbd4-4c41-b371-0a6eee4ae9c5',
'Color': '#FFFF00FF',
'Fluor': 'Alexa Fluor 633',
'ExposureTime': '700000000',
'IlluminationType': 'Epifluorescence',
'ContrastMethod': 'Fluorescence',
'PixelType': 'Gray16',
'ComponentBitCount': '16',
'AcquisitionMode': 'WideField',
'IlluminationWavelength': {'SinglePeak': '630', 'Ranges': '615-648'},
'DetectorSettings': {'Binning': '1,1',
'HasFocusRoi': 'true',
'Detector': {'@id': 'Detector:Hamamatsu Orca Flash'}},
'LightSourcesSettings': {'LightSourceSettings': {'Intensity': '100.00 %',
'LightSource': {'@id': 'LightSource:2'}}},
'FilterSetRef': {'@id': 'FilterSet:2'}},

[lucas-diedrich]

Hi! Thanks for the request, will check it out. Would you expect that you will need different types of information at some point or is this kind of desired information "set in stone"?

[machth]

Maybe the acquired bit of depth and binning would be interesting as well.
Otherwise, I think this should be it. In my opinion, this should give a great overview over the file and how it was acquired.
If there are really specific information needed at a later time point, they can probably be extracted manually from the full metadata.