A histological and image-analysis pipeline for whole mouse spinal cord. SpinalJ pairs cryo-sectioning scaffolds with a 3D reference atlas and Fiji-based registration software to enable high-throughput cell-level analysis across the entire cord.
SpinalJ was developed in collaboration with the laboratories of Jane Dodd and Carol Mason at Columbia University to address a long-standing methodological gap in whole spinal cord analysis. The pipeline integrates three components that together enable comprehensive, high-throughput study of the entire mouse spinal cord.
Together, these tools provide high-throughput analysis of whole mouse spinal cord and enable direct comparison of three-dimensional spatial information across animals and studies. Mapping accuracy has been verified for known neurons, and the platform has been used to reveal previously unknown neuronal distributions.
The original work used the Nikon AZ100 slide scanner with imaging automation by NIS-Elements JOBS and General Analysis.
Fiederling F, Hammond LA, Ng D, Mason C, Dodd J. Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord. Cell Reports Methods 1(5), 100074 (2021).