PT  - JOURNAL ARTICLE
AU  - Morgan S Schwartz
AU  - Jake Schnabl
AU  - Mackenzie Litz
AU  - Benjamin S. Baumer
AU  - Michael Barresi
TI  - ΔSCOPE: A new method to quantify 3D biological structures and identify differences in zebrafish forebrain development
AID  - 10.1101/715698
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 715698
4099  - http://biorxiv.org/content/early/2019/07/26/715698.short
4100  - http://biorxiv.org/content/early/2019/07/26/715698.full
AB  - Research in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the 3D spatial relationships of biological structures, we developed a computational method and program ΔSCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination). Our approach uses the 3D fluorescent signal distribution within a 3D data set and reorients the fluorescent signal to a relative biological reference structure. This approach enables quantification and statistical analysis of spatial relationships and signal density in 3D multichannel signals that are positioned around a well-defined structure contained in a reference channel. We validated the application of ΔSCOPE by analyzing normal axon and glial cell guidance in the zebrafish forebrain and by quantifying the commissural phenotypes associated with abnormal Slit guidance cue expression in the forebrain. Despite commissural phenotypes that disrupt the reference structure, ΔSCOPE is able to detect subtle, previously uncharacterized, changes in zebrafish forebrain midline crossing axons and glia. This method has been developed as a user-friendly, open source program. We propose that ΔSCOPE is an innovative approach to advancing the state of image quantification in the field of high resolution microscopy, and that the techniques presented here are of broad applications to the life science field.