CUBIC-Cloud: An Integrative Computational Framework Towards Community-Driven Whole-Mouse-Brain Mapping
Mano, T.; Murata, K.; Kon, K.; Shimizu, C.; Ono, H.; Shi, S.; Yamada, R. G.; Miyamichi, K.; Susaki, E. A.; Touhara, K.; Ueda, H. R.
Show abstract
Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize and integrate whole mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analysis and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated brain-wide distribution of PV, Sst, ChAT, Th and Iba1 expressing cells. Second, A{beta} plaque deposition in AD model mouse brains were quantified. Third, we reconstructed neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudo-typed Rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Unraveling Microglial Spatial Organization in the Developing Human Brain with DeepCellMap, a Deep Learning Approach Coupled to Spatial Statistics 96%
- High-throughput two-photon volumetric brain imaging in freely moving mice 95%
- Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics 95%
Similar papers in this journal
- BrainTACO: An Explorable Multi-Scale Multi-Modal Brain Transcriptomic And Connectivity Data Resource 95%
- Three-photon in vivo imaging of neurons and glia in the medial prefrontal cortex with sub-cellular resolution 95%
- Unveiling the Functional Connectivity of Astrocytic Networks with AstroNet, a Graph Reconstruction Algorithm Coupled to Image Processing 94%
Similar papers in this journal
- Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain 96%
- Mapping brain-wide excitatory projectome of primate prefrontal cortex at submicron resolution: relevance to diffusion tractography 94%
- High-throughput mapping of single-cell molecular and projection architecture of neurons by retrograde barcoded labelling 94%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.