19Cryo-electron tomography (cryo-ET) is an emerging technique to study the cellular 20 architecture and the structure of proteins at high resolution in situ. Most biological specimens 21 are too thick to be directly investigated and are therefore thinned by milling with a focused 22 ion beam under cryogenic conditions (cryo-FIB). This procedure is unautomated and prone to 23 contaminations, which makes it a tedious and time-consuming process, often leading to 24 suboptimal results. Here, we present new hardware and software tools that overcome the 25 current limitations. We developed a new glove box and a high vacuum cryo transfer system 26 and installed a stage heater, a cryo-shield and a cryo-shutter in the FIB milling microscope. 27This reduces the ice contamination during the transfer and milling process and simplifies the 28 handling of the sample. In addition, we introduce a new software application that automates 29 the key milling steps. Together, these improvements allow for high-quality, high-throughput 30 cryo-FIB milling. This paves the way for new types of experiments, which have been previously 31 considered infeasible. 32 33 34 35