Optical tomography provides three-dimensional data of the measured specimen, while quantitative phase imaging enables measuring the induced phase-shifts. Combining those two technologies makes possible to get three-dimensional refractive index reconstruction. This can be achieved by introducing a scan in the measurement process, which can be done in several ways. We present and compare results of tomographic measurements, taken either in angle-scanning or wavelength-scanning approach, respectively in transmission or in reflection microscopy, in the framework of digital holographic microscopy.