The microbeam system at Tohoku University has been applied to various fields since its installation and is mainly used for biological applications. The primary purpose of this work was to develop a 3D mu-CT, in which a microbeam is used as a monoenergetic point X-ray source. The second one was to develop a microbeam analysis system for biological samples. A beam spot of 0.4 x 0.4 mu m(2) at a beam current of several tens of pA has been produced. However, in our set-up, mu-PIXE/RBS analyses demand beam currents of ca. 100 pA, which restricts the spatial resolution to around I x 1 mu m(2). In order to get higher spatial resolution down to several hundred nm and higher beam current with a several mu m resolution, a triplet lens system was designed and newly installed. This upgrade was carried out simultaneously with the recovery from the damage caused by the great east Japan earthquake. The triplet lens system has larger demagnification and was designed by adding a quadrupole lens to the existing doublet system. Although a beam spot size of 2 x 1 mu m(2) is currently obtained, it has not achieved the performance obtained by the previous doublet system. The doublet system has been recovered to its previous performance and is routinely applied to simultaneous mu-PIXE/RBS analysis in various fields. Recent applications of 3D-PIXE-mu-CT of toxic elements in single cells with the new microbeam system are presented. (C) 2013 Elsevier B.V. All rights reserved.