In radiation therapies using radionuclides emitting short-range particles, such as radioimmunotherapy or boron neutron capture therapy, the biological effects are strongly affected by the heterogeneity of the absorbed dose distribution delivered to tumor cells. The three-dimensional (3D) information of the source distribution at the cellular level is required to accurately determine the absorbed dose distribution to the individual tumor cells. Two-dimensional distribution of cell and nuclide with a resolution of 1 microm can be obtained from individual tissue sections by microautoradiography. To obtain such information in 3D, an ideal approach would be to align the serial tissue sections from a block and analyze all of them. This is straightforward in theory, but extremely difficult in practice. Furthermore, every section in the block has to be processed and analyzed, and the usage of the data from this laborious work is very inefficient. An approach presented here is to estimate the absorbed dose based on individual sections without 3D reconstruction. It is realistically workable since it avoids the most difficult task of alignment for the serial tissue sections. In addition, the absorbed dose can be estimated based on a limited number of noncontiguous sections. The validity of this approach has been tested by a Monte Carlo simulation for two representative radionuclide configurations: (a) a uniform distribution of sources and (b) a cell membrane bound source distribution. With only a limited number of sampling sections, the uncertainties in the dose estimation were estimated to approximately 15% for short-range particles.