System and method for three-dimensional imaging of unstained samples using bright field microscopy

An optical sectioning bright field microscopy system comprising:

• an optical transparent holder adapted to receive an unstained sample, the optical transparent holder with the unstained sample is surrounded with air or an optically transparent liquid or solid;
• an optical microscope, the optical transparent holder with the unstained sample are placed inside the optical microscope, the optical microscope having automated change of focus, a substage condenser fitted with an adjustable aperture iris diaphragm, and a digital camera, said digital camera recording the images of a sample produced by said optical microscope and having an output to provide the information contained in said images of a sample, said optical microscope configured to allow operation in bright field mode and under Kohler illumination, said optical microscope configured to allow adjustment of said iris diaphragm, said optical microscope configured to allow acquisition of Z-stacks of images of said sample by using said automated change of focus of said optical microscope to image a set of different planes of focus within said sample and using said digital camera to record a bright field image representative of each of said different planes of focus;
• one or more digital computers configured to receive the output of said digital camera and recognize said output as said Z-stacks of images of said sample, said one or more digital computers configured to apply a high-pass filter, a pairwise frame subtraction filter, a smoothing filter, and a white top hat filter to said Z-stacks of images of said sample resulting in optical section images of the said sample;
• and
• a reporting apparatus in communication with said one or more digital computers, said reporting apparatus configured to provide a report of said optical section images in the form of digital image stacks, matrices of pixel values, projection images or three-dimensional rendered images.