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Abstract The heterogeneity of brain imaging methods in neuroscience provides rich data that cannot be captured by a single technique, and our interpretations benefit from approaches that enable easy comparison both within and across different data types. For example, comparing brain-wide neural dynamics across experiments and aligning such data to anatomical resources, such as gene expression patterns or connectomes, requires precise alignment to a common set of anatomical coordinates. However, this is challenging because registeringin vivofunctional imaging data toex vivoreference atlases requires accommodating differences in imaging modality, microscope specification, and sample preparation. We overcome these challenges inDrosophilaby building anin vivoreference atlas from multiphoton-imaged brains, called the Functional Drosophila Atlas (FDA). We then develop a two-step pipeline, BrIdge For Registering Over Statistical Templates (BIFROST), for transforming neural imaging data into this common space and for importingex vivoresources such as connectomes. Using genetically labeled cell types as ground truth, we demonstrate registration with a precision of less than 10 microns. Overall, BIFROST provides a pipeline for registering functional imaging datasets in the fly, both within and across experiments. SignificanceLarge-scale functional imaging experiments inDrosophilahave given us new insights into neural activity in various sensory and behavioral contexts. However, precisely registering volumetric images from different studies has proven challenging, limiting quantitative comparisons of data across experiments. Here, we address this limitation by developing BIFROST, a registration pipeline robust to differences across experimental setups and datasets. We benchmark this pipeline by genetically labeling cell types in the fly brain and demonstrate sub-10 micron registration precision, both across specimens and across laboratories. We further demonstrate accurate registration betweenin-vivobrain volumes and ultrastructural connectomes, enabling direct structure-function comparisons in future experiments.
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High-speed whole-brain imaging in Drosophila
Abstract Recent advances in brain-wide recordings of small animals such as worms, fish, and flies have revealed complex activity involving large populations of neurons. In theDrosophilabrain, with about 140,000 neurons, brain-wide recordings have been critical to uncovering widespread sensory and motor activity. However, current limitations in volumetric imaging rates hinder the accurate capture of fast neural dynamics. To improve the speed of volumetric imaging inDrosophila, we leverage the recently introduced light beads microscopy (LBM) method. We built a microscope and a LBM module tailored to fly brain experiments and used it to record brain-wide calcium signals in adult behaving flies at either 28 volumes per second or at 60 volumes per second (when selecting the central brain alone). We uncover fast-timescale auditory responses that are missed with standard volumetric imaging. We also demonstrate how temporal super-resolution can be combined with LBM data to uncover responses to singleDrosophilacourtship song pulses. This establishes LBM as a viable tool for capturing whole-brain activity at high spatial and temporal resolution in the fly.
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- Award ID(s):
- 1734030
- PAR ID:
- 10672173
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Posted Content:
- https://doi.org/10.1101/2025.06.18.660371
