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About fly-1

Information about the fly-1 data set.

Summary

This dataset contains whole brain calcium or voltage recordings of adult Drosophila. They were recorded with light field microscopy, which permits ultra-fast whole-brain acquisition (up to 200Hz) albeit at lower spatial resolution than other techniques such as confocal microscopy. In some of the calcium data, the fly was behaving (mostly walking or grooming) and the behavior data is included. Other voltage and calcium datasets present response to stimuli (puffs of odor or flashes of UV light).

One recording typically lasted one or two minutes. There are around 5 flies per condition. The whole brain fluorescence recordings are in NifTI format, and can be opened in ImageJ using the NifTI Input/Output plugin, with matlab using MRIread, or with python using nibabel (see scripts provided). Examples of alignment to an anatomical template, as well as results from source extraction using PCA/ICA are also provided.

See also a github repository: https://github.com/sophie63/FlyLFM, as well as a publication based on this dataset:

Fast near-whole brain imaging in adult Drosophila during responses to stimuli and behavior. Sophie Aimon, Takeo Katsuki, Tongqiu Jia, Logan Grosenick, Michael Broxton, Karl Deisseroth, Terrence J. Sejnowski, Ralph J Greenspan bioRxiv 033803; doi: https://doi.org/10.1101/033803

Format of the data

The data are stored mostly in NifTI format. Details are given in the data description document listed at the bottom of this page.  Total data size is about 965 GB.

Conditions for using the data

This dataset is shared under a Creative Commons Attribution 4.0 International license. If you publish any work using the data, please cite the publication referenced above (Aimon et al.), and also cite the dataset using the following:

Sophie Aimon, Takeo Katsuki, Tongqiu Jia, Logan Grosenick, Michael Broxton, Karl Deisseroth, Terrence J. Sejnowski, Ralph J Greenspan (2019); Whole-brain recordings of adult Drosophila using light field microscopy along with corresponding behavior or stimuli data. CRCNS.org
http://dx.doi.org/10.6080/K01J97ZN
Note that Sophie Aimon (aimon.sophie@gmail.com) would appreciate being consulted before publication.

 

The above citation uses a Digital Object Identifier (DOI) which is assigned to the data set.  The DOI was created using DataCite (www.datacite.org) and the California Digital Library, "EZID" system (n2t.net/ezid/).

How to download the data

The data may be downloaded from:
https://portal.nersc.gov/project/crcns/download/fly-1
Using a CRCNS.org account.  See the download link for more information about downloading.

Getting help using the data.

If you have questions about using the data, post them on the forum for using data sets.

Documentation files

crcns_fly-1_data_description.pdf

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