Add function to extract ROIs metadata from ScanImage tiff

In the ScanImage .tif metadata there is a dictonary saved as text that the function extract_extra_metadata cannot parse, where information on the ROIs are stored. I implemented a new function call extract_roi_metadata (https://github.com/catalystneuro/roiextractors/pull/272) that return this dict.

"RoiGroups":{
    "imagingRoiGroup":{# general imaging space metadata (only 2D)
        ...
        "centerXY": [-1.776356839e-16,0.1],
        "sizeXY": [13.5,13.5], # size of the FOV in micrometers
        "rotationDegrees": 0,
        "enable": 1,
        "pixelResolutionXY": [512,512],
        "pixelToRefTransform": [[0.0263671875,0,-6.763183594],
                                [0,0.263671875,-6.663183594],
                                [0,0,1]],
        "affine":  [[13.5,0,-6.75],
                    [0,13.5,-6.65],
                    [0,0,1]]
        ...
    },
    "integrationRoiGroup":{
        ...
        "rois": [
        {
          "ver": 1,
          "classname": "scanimage.mroi.Roi",
          "name": "ROI 1",
            ...
          "zs": 0,
          "scanfields": {
            ...
            "centerXY": [2.518066406,1.062402344],
            "sizeXY": [0.2373046875,0.2373046875],
            "rotationDegrees": 0,
            "enable": 1,
            "threshold": 100,
            "channel": 1,
            "processor": "cpu",
            "mask": [roi_pixel_mask 9x9 binary matrix],
            "affine": [[0.2373046875,0,2.518066406],
                       [0,0.2373046875,1.062402344],
                       [0,0,1]]
          },
          "discretePlaneMode": 1,
          "powers": null,
          "pzAdjust": null,
          "Lzs": null,
          "interlaceDecimation": null,
          "interlaceOffset": null,
          "enable": 1
        },
        ... # all the 368 ROIs
        ]
    } # imaging space metadata for each ROI
}

From imagingRoiGroup we can extract info on the dimension of the field of view (XY) from "sizeXY" and divide by the dimension to get the grid_spacing (z dimension missed)

In integrationRoiGroup we can extract information about the position of the rois: inv(pixelToRefTransform)*centerXY

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catalystneuro / roiextractors

Add function to extract ROIs metadata from ScanImage tiff #272

Codecov Report