SCAPE Microscopy for High Speed, 3D Whole-Brain Imaging in Drosophila Melanogaster

Li, Wenze; Voleti, Venkatakaushik; Schaffer, Evan; Vaadia, Rebecca Danielle; Grueber, Wesley B.; Mann, Richard S.; Hillman, Elizabeth M. C.

doi:10.1364/brain.2016.btu4d.3

Cited by 7 publications

(4 citation statements)

References 4 publications

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“…Faster techniques have also been used to image large-scale activity in flies: [27] used a Bessel beam to image 25% of the brain at 3.6 Hz, and [28] used a light sheet approach (swept confocally aligned planar excitation [SCAPE]) to image a large portion of the brain at 10 Hz. To test whether the fast-frame rate of the light field method enabled detecting signals otherwise undetectable with slower imaging methods, we subtracted the data smoothed over 100 ms, thus revealing only the activity above 10 Hz.…”

Section: Resultsmentioning

confidence: 99%

Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior

Aimon¹,

Katsuki²,

et al. 2019

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Whole-brain recordings give us a global perspective of the brain in action. In this study, we describe a method using light field microscopy to record near-whole brain calcium and voltage activity at high speed in behaving adult flies. We first obtained global activity maps for various stimuli and behaviors. Notably, we found that brain activity increased on a global scale when the fly walked but not when it groomed. This global increase with walking was particularly strong in dopamine neurons. Second, we extracted maps of spatially distinct sources of activity as well as their time series using principal component analysis and independent component analysis. The characteristic shapes in the maps matched the anatomy of subneuropil regions and, in some cases, a specific neuron type. Brain structures that responded to light and odor were consistent with previous reports, confirming the new technique’s validity. We also observed previously uncharacterized behavior-related activity as well as patterns of spontaneous voltage activity.

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Section: Resultsmentioning

confidence: 99%

Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior

Aimon¹,

Katsuki²,

et al. 2019

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“…Population recordings have now been used to elucidate mechanisms behind zebra finch song production [1], spatial encoding in mice [2], and limb movement in primates [3]. When applied to small transparent organisms, like Caenorhabditis elegans [4], Drosophila [5], and zebrafish [6], nearly every neuron in the brain can be recorded, permitting the study of whole brain neural dynamics at cellular resolution.…”

Section: Introductionmentioning

confidence: 99%

Automatically tracking neurons in a moving and deforming brain

et al. 2017

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Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must be tracked in 3D over time to accurately extract single neuron activity traces. Recordings from small invertebrates like C. elegans are especially challenging because they undergo very large brain motion and deformation during animal movement. Here we present an automated computer vision pipeline to reliably track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. 3D volumetric fluorescent images of the animal’s brain are straightened, aligned and registered, and the locations of neurons in the images are found via segmentation. Each neuron is then assigned an identity using a new time-independent machine-learning approach we call Neuron Registration Vector Encoding. In this approach, non-rigid point-set registration is used to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. The way each neuron matches with the references defines a feature vector which is clustered to assign an identity to each neuron in each volume. Finally, thin-plate spline interpolation is used to correct errors in segmentation and check consistency of assigned identities. The Neuron Registration Vector Encoding approach proposed here is uniquely well suited for tracking neurons in brains undergoing large deformations. When applied to whole-brain calcium imaging recordings in freely moving C. elegans, this analysis pipeline located 156 neurons for the duration of an 8 minute recording and consistently found more neurons more quickly than manual or semi-automated approaches.

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“…The preparation described above allows observation of the whole brain under a microscope for large scale 3D imaging such as classical 2 photons or confocal microscopy, but also faster techniques such as light sheet 31 and other structured illumination microscopy techniques (reviewed in 32 ), or light field microscopy 28 .…”

Section: Representative Resultsmentioning

confidence: 99%

Preparing Adult <em>Drosophila melanogaster</em> for Whole Brain Imaging during Behavior and Stimuli Responses

Woller

Bandow

Aimon

et al. 2021

JoVE

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We present a method developed specifically to image the whole Drosophila brain during ongoing behavior such as walking. Head fixation and dissection are optimized to minimize their impact on behavior. This is first achieved by using a holder that minimizes movement hindrances. The back of the fly's head is glued to this holder at an angle that allows optical access to the whole brain while retaining the fly's ability to walk, groom, smell, taste and see. The back of the head is dissected to remove tissues in the optical path and muscles responsible for head movement artefacts.The fly brain can subsequently be imaged to record brain activity, for instance using calcium or voltage indicators, during specific behaviors such as walking or grooming, and in response to different stimuli. Once the challenging dissection, which requires considerable practice, has been mastered, this technique allows to record rich data sets relating whole brain activity to behavior and stimulus responses.

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SCAPE Microscopy for High Speed, 3D Whole-Brain Imaging in Drosophila Melanogaster

Cited by 7 publications

References 4 publications

Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior

Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior

Automatically tracking neurons in a moving and deforming brain

Preparing Adult <em>Drosophila melanogaster</em> for Whole Brain Imaging during Behavior and Stimuli Responses

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