GarnerKindLai_MeTu paper https://www.nature.com/articles/s41586-024-07967-z
All EM analyses were performed in MacOS using R and Python. All calcium imaging analyses were performed in Windows using Matlab.
Natverse https://natverse.org
Tidyverse https://www.tidyverse.org/
alphashape3d https://CRAN.R-project.org/package=alphashape3d
numpy https://numpy.org/install/
pandas https://pandas.pydata.org/docs/getting_started/index.html
matplotlib https://matplotlib.org/stable/
seaborn https://seaborn.pydata.org/installing.html
pydantic https://docs.pydantic.dev/latest/install/
scipy https://scipy.org/install/
navis https://navis.readthedocs.io/en/latest/source/install.html
caveclient https://caveclient.readthedocs.io/en/latest/guide/intro.html
cloudvolume https://github.com/seung-lab/cloud-volume
pymaid https://github.com/schlegelp/PyMaid
FAFBseg https://github.com/flyconnectome/fafbseg-py
bokeh https://docs.bokeh.org/en/latest/docs/first_steps.html#first-steps
holoviews https://www.holoviews.org/
hvplot https://hvplot.holoviz.org/getting_started/installation.html
neuprint https://connectome-neuprint.github.io/neuprint-python/docs/
Computer Vision Toolbox
Image Processing Toolbox
Optimization Toolbox
Statistics and Machine Learning Toolbox
All necessary packages for R, Python, and Matlab should be installed. Installation instructions can be found at homepages of those packages. We used the most recent packages as of March, 2024. Installation time for these packages depend on the computer specification. Please see the homepage of each packages.
There is no required hardware other than a computer that can run R, Python, and Matlab (most recent versions as of March, 2024).
Git clone or download the current repository. Cloning or downloading time is typically less than 1 minute.
EM analyses: Run the main script in the folder to replicate analyses and produce figures. Each section of code analyze the data and generate figures. The analyses time varies widely (some analyses, such as scanning the entire database to identify visual pathways to the central complex, may take a few hours).
Two-photon calcium imaging: Run plot_script files in each of the figure folder to generate plots in the figures. (Raw imaging files will be provided upon request. Intermediate data files are available in each folder.)
Users must have a FlyWire account and an API token to run EM analyses code. Visit https://flywire.ai for more details.
Some analysis code requires large spreadsheet files (cannot be uploaded to GitHub because of their size) to proceed. The final versions of those files will be available in DRYAD by the time of publication and linked to this page.