reader specifications
ReaderSpecsABC
ReaderSpecsABC ()
Helper class that provides a standard way to create an ABC using inheritance.
MicroscopyReaderSpecs
MicroscopyReaderSpecs ()
Helper class that provides a standard way to create an ABC using inheritance.
ROIReaderSpecs
ROIReaderSpecs ()
findmycells enables analyses of multiple ROIs in the image data. To do so, they will be matched based on their ID that will be retrieved from the ROI file. Some softwares that create these ROI-files, however, create default IDs for the individual ROIs that will interfere with this matching. For instance, in Fiji / ImageJ2, created ROIs get its centroid (?) pixel coordinates as default ID (e.g. something like “523-378”). Since such default IDs most likely won´t be consistent throughout your entire image dataset, findmycells provides you with two options to adress this: a) You can set ‘load_roi_ids_from_file’ to False (default): This will cause findmycells to ignore the IDs of the ROIs that are saved in the provided ROI file and assign them with new IDs starting at “000”. Note: Essentially, this requires you to have always the same type of ROIs present in the exact same order in all your ROI-files. It is therefore only recommended if you have just a single ROI you´d like to analyze. b) You can set ‘load_roi_ids_from_file’ to True (recommended if you have more than a single ROI): This will enforce that findmycells uses the IDs that each ROI was saved with. Therefore, it requires that you use consistent naming of the ROIs with your preferred software. For instance, if you´re using Fiji / ImageJ2, you can rename each ROI in the ROIManager (e.g. “CA3”, “vlPAG”, or “ipsilateral_SNc”). Analyses and quantifications will then be matched and pooled across all ROIs with the respective IDs (e.g. all “CA3” ROIs).