ΔSCOPE: A new method to quantify 3D biological structures and identify differences in zebrafish forebrain development
Abstract
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 three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called SCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination). Our approach uses the 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 SCOPE 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 which display disruptions to the reference structure, SCOPE was 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 SCOPE 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.
Additional Information
© 2020 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received 30 July 2019, Revised 14 November 2019, Accepted 26 November 2019, Available online 24 December 2019. We would like to thank the generous contributions of Melissa Hardy and the late Chi-Bin Chien to this research in their development and donation of the heatshock (hsp70) responsive slit1a tghsp70:slit1a:mcherry and tghsp70:mcherry lines. We would like to Nadia PenkoffLiedbeck, Cassie Kemmler, and Jin-Sook Park for their substantial contributions to data collection and project assistance. We would also like to thank Margaret Perry, Audrey Bertin, Kalynn Kosyka, Crystal Zang, Emma Ning for their assistance reviewing the code base and providing technical assistance weeding out errors. This work would not have been possible without the generous contributions of time and effort by the Smith College Center for Microscopy and its director, Judith Wopereis, and the Smith Animal Care facility. We are very thankful for all of the technical support provided by Alicia Famiglietti and all constructive discourse by the entire Barresi lab throughout this work. No competing interests declared. Author Contribution: MJFB, JS, and MSS conceived the project. BSB, JS, and MSS developed the methodology. MPHL, MS wrote the code. MPHL and JS performed experiments and collected data. JS annotated training data for ilastik pixel classification. MPHL, JS, and MS corrected commissure alignments. JS and MS wrote the original draft. MJFB, MPHL, and JS revised the final draft. MJFB and BSB supervised the project. MJFB funded the project. This work was supported by the National Institutes of Health [HD060023]; the National Science Foundation [IOS-1656310]; and graduate student funding from the University of Massachusetts Amherst IDGP.Attached Files
Published - 1-s2.0-S0012160619304609-main.pdf
Submitted - 715698.full.pdf
Supplemental Material - 1-s2.0-S0012160619304609-mmc1.zip
Supplemental Material - 1-s2.0-S0012160619304609-mmc2.pdf
Supplemental Material - 1-s2.0-S0012160619304609-mmc3.docx
Supplemental Material - 1-s2.0-S0012160619304609-mmc4.xml
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Additional details
- Alternative title
- DeltaSCOPE
- Eprint ID
- 99891
- Resolver ID
- CaltechAUTHORS:20191118-091158530
- HD060023
- NIH
- IOS-1656310
- NSF
- University of Massachusetts
- Created
-
2019-11-18Created from EPrint's datestamp field
- Updated
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2023-06-01Created from EPrint's last_modified field