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These results demonstrate the use of a high resolution scanner for rapid screening of cellular responses (number and morphology) to 3D biomaterials for neural tissue engineering applications. Limited axonal re-growth through the injury site has been linked to poor Schwann cell (SC) migration and re-population. An optimal biomaterial that promotes neurite outgrowth and SC migration may improve functionality. In this work, a fluorescence flatbed scanner was used to rapidly assess cells in 3D, using SC as a model cell. Assay sensitivity to size, cell number, and material was examined using primary SCs cultured for 1-3 days. The cultured arrays were fixed, immunostained, and scanned. Increased spot intensities on the scanned arrays were identified as `hits', which were confirmed with traditional fluorescence microscopy. There were no differences in scanning for constructs 2-4 mm. Significant differences were detected in cell number for 250-1000 cells/μl. More subtle differences in cell spreading were detected below 1000 cells/μl, confirmed by traditional fluorescence microscopy. Morphological differences were detected using the scanner between the two model biomaterials (collagen-Matrigel™ and collagen-only materials) These results demonstrate the feasibility of using a scanner to rapidly assess complex protein arrays to screen large libraries of biomaterials in 3D for use in tissue engineering.