Methods and Systems for Imaging a Biological Sample

A method for imaging a biological sample, the method comprising:

• a) scanning a biological sample using one or more light sheets, wherein
• the biological sample, or a portion thereof, is in a field of view of a microscope comprising an objective having an objective refractive index, wherein a direction of observation of the objective defines a z-axis and a medium is disposed between the sample and the objective, thereby illuminating a plurality of z-axial slices of the biological sample, each z-axial slice having an average slice thickness in the z-axial direction,
• wherein
• the medium has a refractive index that is different from the objective refractive index, and
• the biological sample is at a z-axial distance from the objective;
• and
• b) recording a plurality of images corresponding to the plurality of z-axial slices of the sample, wherein the plurality of images are generated by a plurality of light patterns emitted from the scanned biological sample, thereby generating an image stack comprising a plurality of images of the biological sample, or a portion thereof.