SlicesMapi: An Interactive Three-Dimensional Registration Method for Serial Histological Brain Slices

Agarwal, N., Xu, X., & Gopi, M. (2018). Geometry processing of conventionally produced mouse brain slice images[J]. Journal of Neuroscience Methods, 306, 45–56.

Article  PubMed  PubMed Central  Google Scholar 

Amato, S. P., Pan, F., Schwartz, J., et al. (2016). Whole brain imaging with serial two-photon tomography[J]. Frontiers in Neuroanatomy, 10, 31.

Article  PubMed  PubMed Central  Google Scholar 

Avants, B. B., Epstein, C. L., Grossman, M., et al. (2008). Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain[J]. Medical Image Analysis, 12(1), 26–41.

Article  CAS  PubMed  Google Scholar 

Cao R, Ling Y, Meng J, et al. SMDB: a Spatial Multimodal Data Browser[J]. Nucleic Acids Research, 2023: gkad413.

Carey, H., Pegios, M., Martin, L., et al. (2023). DeepSlice: Rapid fully automatic registration of mouse brain imaging to a volumetric atlas[J]. Nature Communications, 14(1), 5884.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, J., & Ke, R. (2024). Spatial analysis toolkits for RNA in situ sequencing. Wiley Interdiscip Rev RNA., 15(2), e1842.

Article  CAS  PubMed  Google Scholar 

Chen, S., Liu, Z., Li, A., et al. (2021). High-throughput strategy for profiling sequential section with multiplex staining of mouse brain[J]. Frontiers in Neuroanatomy, 15, 771229.

Article  PubMed  PubMed Central  Google Scholar 

Chie J A K C, Persohn S C, Miner E W, et al. Total Variation Based 2D Image Registration of Post-Mortem Mouse Brain Images[C]//2024 IEEE International Symposium on Biomedical Imaging (ISBI). IEEE, 2024: 1–4.

Ferrante, E., & Paragios, N. (2017). Slice-to-volume medical image registration: A survey[J]. Medical Image Analysis, 39, 101–123.

Article  PubMed  Google Scholar 

Fuglstad, J. G., Saldanha, P., Paglia, J., & Whitlock, J. R. (2023). Histological E-data Registration in rodent Brain Spaces. eLife, 13(12), e83496.

Article  Google Scholar 

Gong, H., Xu, D., Yuan, J., et al. (2016). High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level[J]. Nature Communications, 7(1), 12142.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hou, B., Alansary, A., McDonagh, S. et al (2017). Predicting slice-to-volume transformation in presence of arbitrary subject motion[C]. Medical Image Computing and Computer-Assisted Intervention− MICCAI 2017: 20th International Conference, Quebec City, QC, Canada, September 11-13, 2017, Proceedings, Part II 20. Springer International Publishing, 296-304.

Huszar, I. N., Pallebage-Gamarallage, M., Bangerter-Christensen, S., et al. (2023). Tensor image registration library: Deformable registration of stand-alone histology images to whole-brain post-mortem MRI data[J]. NeuroImage, 265, 119792.

Article  PubMed  Google Scholar 

Kurz, A., Müller, H., Kather, J. N., et al. (2024). 3-dimensional reconstruction from histopathological sections: A systematic review[J]. Laboratory Investigation, 104(6), 102049.

Article  PubMed  Google Scholar 

Ni, H., Feng, Z., Guan, Y., et al. (2021). DeepMapi: A fully automatic registration method for mesoscopic optical brain images using convolutional neural networks[J]. Neuroinformatics, 19, 267–284.

Article  PubMed  Google Scholar 

Puchades, Maja A., et al. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PloS one,2019,14.5: e0216796.

Rodriques, S. G., Stickels, R. R., Goeva, A., et al. (2019). Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science, 363(6434), 1463–1467.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ronneberger, O., Fischer, P., Brox, T. (2015). U-net: Convolutional networks for biomedical image segmentation[C]. Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015: 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part III 18. Springer International Publishing 234-241

Sadeghi, M., Ramos-Prats, A., Neto, P., et al. (2023). Localization and Registration of 2D Histological Mouse Brain Images in 3D Atlas Space[J]. Neuroinformatics, 21(3), 615–630.

Article  PubMed  PubMed Central  Google Scholar 

Schoop, R. A. L. de Roode, L. M. de Boer, L. L. et al (2024). Framework for deep learning based Multi-Modality image registration of snapshot and pathology images[J]. IEEE Journal of Biomedical and Health Informatics.

Smart, A., Tisca, C., Huszar, I. N., et al. (2023). Protocol for tissue processing and paraffin embedding of mouse brains following ex vivo MRI[J]. STAR Protocols, 4(4), 102681.

Article  PubMed  PubMed Central  Google Scholar 

Song, J. H., Choi, W., Song, Y. H. et al. (2020). Precise mapping of single neurons by calibrated 3D reconstruction of brain slices reveals topographic projection in mouse visual cortex[J]. Cell Reports 31(8).

Wang, Q., Ding, S. L., Li, Y. et al (2020) The Allen mouse brain common coordinate framework: a 3D reference atlas[J]. Cell 181(4): 936–953. e20.

Xu, J., Moyer, D., Grant, P. E. et al (2022). SVoRT: iterative transformer for slice-to-volume registration in fetal brain MRI[C]. International Conference on Medical Image Computing and Computer-Assisted Intervention. Cham: Springer Nature Switzerland 3–13.

Yang, Z., Richards, K., Kurniawan, N. D., et al. (2012). MRI-guided volume reconstruction of mouse brain from histological sections[J]. Journal of Neuroscience Methods, 211(2), 210–217.

Article  PubMed  Google Scholar 

Yates, Sharon C., et al. QUINT: workflow for quantification and spatial analysis of features in histological images from rodent brain. Frontiers in neuroinformatics,2019,13: 75.

Zhong, Q., Li, A., Jin, R., et al. (2021). High-definition imaging using line-illumination modulation microscopy[J]. Nature Methods, 18(3), 309–315.

Article  CAS  PubMed  Google Scholar 

Comments (0)

No login
gif