High-Throughput Automated Microscopy Platform for the Allen Brain Atlas

The Allen Brain Atlas (ABA) is a genomic scale, web-based 3D atlas of expression of more than 20,000 genes in the mouse brain visualized using colorimetric in situ hybridization. Completing the ABA required imaging more than 1 million individual brain sections at cellular resolution. To facilitate these imaging needs, a high throughput, fully scalable, automated microscopy platform capable of imaging more than 3000 brain sections daily was developed. This system runs 24 h per day and 7 days per week with minimal operator supervision. The platform comprises a barcode scanner, fully automated microscope, stage, slide loader, digital camera, and custom software for managing the microscopy process. When operating at full capacity, the imaging system generates approximately one terabyte of uncompressed image data daily. Image data from the platform are freely available as part of the ABA online.