readers for microscopy images
MicroscopyImageReaders
MicroscopyImageReaders ()
The read method of MicroscopyImageReaders subclasses has to return a numpy array with the following structure: [imaging-planes, rows, columns, color-channels] For instance, an array of a RGB z-stack with 10 image planes of 1024x1024 pixels will have a shape of: [10, 1024, 1024, 3] To improve re-usability of the same functions for all different kinds of input images, this structure will be used even if there is just a single plane. For instance, the shape of the array of a grayscale 2D image with 1024 x 1024 pixels will look like this: [1, 1024, 1024, 1]
CZIReader
CZIReader ()
This reader enables loading of images acquired with the ZEN imaging software by Zeiss, using the czifile package. Note: czifile returns numpy arrays of different shapes depending on the imaging conditions. As an example: if z-stack images were acquired, there is on dimension more than for plane images. As the czifile-function CziFile.asarray() behaves rather unpredictable - for the reasons mentioned above -, it could well be, that there are other format shapes, that are not taken into account in the if-elif-else loop in self.read(). Please note, that the else condition in self.read() was not tested yet, as there was no matching test data at hand! If the CZIReader throws an error at your data, feel free to open up an issue or to add a solution in a pull request!
RegularImageFiletypeReader
RegularImageFiletypeReader ()
This reader enables loading of all regular image filetypes, that scikit-image can read, using the scikit-image.io.imread function. Note: So far only single plane images are supported (yet, both single-color & multi-color channel images are supported)!
FromExcelReader
FromExcelReader ()
This reader is actually only a wrapper to the other MicroscopyImageReaders subclasses. It can be used if you stored the filepaths to your individual plane images in an excel sheet, for instance if you were using our “prepare my data for findmycells” functions. Please be aware that the corresponding datatype has to be loadable with any of the corresponding MicroscopyImageReaders!