Connectomics may play an important role in understanding how neuroanatomy is related to brain function in mammals. In particular EM-driven saturated reconstruction is potentially indispensable for determining brain wiring diagrams. We are developing Automatic Tape-collecting Ultra-Microtome (ATUM)-SEM to acquire serial section images (typically 4 nm x 4nm x 30 nm resolution) and reconstructing the cellular processes using automatic segmentation algorithms. I will emphasize three challenges in this talk: big image data analysis, data precision and correlative microscopy. 1) So far, we have achieved 40 MHz data acquisition rate in 5% of 1mm³ mouse brain region. Once a 61 multiple beam SEM (mSEM) is installed, the image acquisition rate is dramatically increased to greater than 1 GHz, which means only 3 weeks for acquiring 1mm³ brain volume. This forces more complicated image acquisition strategies and more sophisticated image data management. Development of a completely automated system is needed throughout the entire data acquisition process. Moreover, the following data analysis process, including image alignment and feature extraction, should be more effective to keep pace with the mSEM data acquisition speed. 2) In terms of precision of image data, the Z resolution is substantially worse due to the limitation of slice thickness (30 nm) with diamond cutting. In order to enhance the image accuracy of the neuronal reconstruction, some computer tomography techniques should be applied. We are trying to increase Z resolution to values thinner than the physical section thickness with a multiple-energy beam imaging method. 3) The correlative microscopy of both EM and light microscopy should be developed to identify the molecules related to neural functions on the map of the finest wiring diagrams. To establish the correlative microscopy with ATUM, the feature of collecting tape is a key issue to be improved in terms of flatness, conductivity and autofluorescence. We are seeking a new material as an alternative to the conventional Kapton tape, which is nano-scale flat, electron-resistant, less autofluorescence and transparent plastic or glass tapes with conductive coating. The finding of an improved material for ATUM correlative microscopy is one of the big challenges that remain to achieve multi-modal imaging.