readers for ROI-files

Extends the generic reader classes for specific ROI data types (findmycells.readers.rois)

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ROIReaders

 ROIReaders ()

Return the roi(s) as shapely.geometry.Polygon(s) in a nested dictionary with structure: {plane_id: {roi_id: Polygon}} In case plane-specific ROIs are required / requested at some point, having the additional level that enables the reference to plane_id(s) should foster the implementation. The current implementation, however, only supports the use of ROIs for all planes - the corresponding plane_id is hence: ‘all_planes’ Ultimately, this file_id specific dictionary can then be integrated into the ‘rois_as_shapely_polygons’ attribute of the database.

Note: If multiple ROIs are used for one image, the individual ROIs must be named properly in the ROIManager-Tool in ImageJ. For instance, if images of the hippocampus are investigated & they can contain images of the DG, CA3 and CA1, the corresponding ROIs that mark the respective area have to be named consistenly for all .zip files. This makes it possible, that findmycells can handle the analysis even if not all ROIs are present for each image, e.g. for some files only DG and CA3.

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ImageJROIReader

 ImageJROIReader ()

Return the roi(s) as shapely.geometry.Polygon(s) in a nested dictionary with structure: {plane_id: {roi_id: Polygon}} In case plane-specific ROIs are required / requested at some point, having the additional level that enables the reference to plane_id(s) should foster the implementation. The current implementation, however, only supports the use of ROIs for all planes - the corresponding plane_id is hence: ‘all_planes’ Ultimately, this file_id specific dictionary can then be integrated into the ‘rois_as_shapely_polygons’ attribute of the database.

Note: If multiple ROIs are used for one image, the individual ROIs must be named properly in the ROIManager-Tool in ImageJ. For instance, if images of the hippocampus are investigated & they can contain images of the DG, CA3 and CA1, the corresponding ROIs that mark the respective area have to be named consistenly for all .zip files. This makes it possible, that findmycells can handle the analysis even if not all ROIs are present for each image, e.g. for some files only DG and CA3.