Computer-implemented systems and methods for processing image data of a process-free plate are provided according to the present disclosure. The systems and methods may, generally, include a data acquisition step/means for receiving image data using one or more channels of a imaging system, each channel functioning to image the same target region of a process-free plate using a different wavelength of light, and a data processing step/means for filtering the image data using at least one of: (i) self-filtering, (ii) Fourier shrinkage and (iii) Wavelet shrinkage. When the image data is received using a plurality of channels, the received image data may advantageously be combined so as to optimize contrast-to-noise performance. The disclosed systems and methods may advantageously perform the operations of image de-noising, contrast enhancement, and thresholding, and may further involve compensation techniques, e.g., for minimizing distortion and blurring effects.