If you use optical microscopy you the axial resolution in Z (depth of focus) is limited by the microscope objective have a look for example to the Abbe equation.
Abbe Resolution_z = 2 lambda/NA^2 where NA is the numerical aperture of the microscope objective
Solution to extent the depth of focus is using digital holographic microscope.
You'll struggle to image at those depths without two photon/light sheet, and even then this will depend on how scattering the tissue is. In any case, most turn key systems will allow you to increase laser power/detector sensitivity with increasing z-depth, allowing some correction for illumination changes.