Here I’ve compiled a memo-style list of research tools useful for working with the fruit fly (Drosophila).
If anything is missing, or if there is a tool you would like me to add, please leave a comment on the site or contact me at haya.m.yamano.neuro@gmail.com.
This page is still under construction, so the information will keep growing over time.
Last updated: December 1, 2023
Databases
FlyBase
URL: https://flybase.org
A comprehensive database for Drosophila. In addition to gene sequences and expression data, it provides access to research papers and information about the Drosophila research community.
FlyWire
URL: https://flywire.ai
NeuronBridge
URL: https://neuronbridge.janelia.org
FlyLight
URL: https://www.janelia.org/project-team/flylight
FlyCircuit
URL: https://www.flycircuit.tw
neuPrint
URL: https://neuprint.janelia.org
SCope
URL: https://scope.aertslab.org
Fly Cell Atlas
Paper:
Stock Centers
Bloomington Drosophila Stock Center
The Drosophila stock center at Indiana University in Bloomington, USA.
You can search not only by genotype but also by stock number (the numbers beginning with BL).
A wide variety of lines are available here, including GAL4, UAS, and RNAi lines.
Vienna Drosophila Resource Center
URL: https://shop.vbc.ac.at/vdrc_store/
The Drosophila stock center at the Institute of Molecular Biotechnology (IMBA) in Austria. It holds an especially large collection of RNAi lines.
KYOTO Drosophila Stock Center
URL: https://kyotofly.kit.jp/cgi-bin/stocks/index.cgi
A stock center at the Kyoto Institute of Technology in Kyoto, Japan. It is the largest Drosophila stock center in Japan; you can download the stock list from the site and search collectively by line.
KYORIN-Fly : Drosophila species stock center
URL: https://shigen.nig.ac.jp/fly/kyorin/
A Drosophila stock center at Kyorin University in Japan. It maintains a wide range of Drosophila species, and mutants of species closely related to Drosophila melanogaster can also be obtained here.
Behavioral Analysis Tools
DeepLabCut
URL: http://www.mackenziemathislab.org/deeplabcut
Paper: Mathis A, Mamidanna P, Cury KM, et al. DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nat Neurosci. 2018;21(9):1281-1289. DOI:10.1038/s41593-018-0209-y
SLEAP
URL: https://sleap.ai
Paper: Pereira TD, Tabris N, Matsliah A, et al. SLEAP: A deep learning system for multi-animal pose tracking. Nat Methods. 2022;19(4):486-495.
DOI:10.1038/s41592-022-01426-1
UMATracker
URL: https://ymnk13.github.io/UMATracker/
Paper: Yamanaka O, Takeuchi R. UMATracker: An intuitive image-based tracking platform. J Exp Biol. 2018;221(16):1-5.
DOI:10.1242/jeb.182469
Ctrax
URL: https://ctrax.sourceforge.net
Paper: https://www.nature.com/articles/nmeth.1328
FlyTracker
URL:
Paper:
ID Tracker
URL:
Paper:
TRex
URL:
Paper: https://elifesciences.org/articles/64000
JAABA
URL:
Paper:
Other Resources
Brain and VNC template (JRC 2018 Brain templates)
URL: https://www.janelia.org/open-science/jrc-2018-brain-templates
Color-Depth MIP
URL: https://www.janelia.org/open-science/color-depth-mip
Dissection and Immunostaining Protocols
URL: https://www.janelia.org/project-team/flylight/protocols
Here you can find videos on dissecting adult and larval Drosophila, along with immunostaining protocols.