# The Brain And Nerve Cord fly connectome
The BANC (pronounced "bank") is the Brain And Nerve Cord, a GridTape-TEM dataset of an adult _Drosophila melanogaster_'s entire central nervous system. This dataset was generated by [Jasper Phelps](http://jasper.science) and [Minsu Kim](https://www.linkedin.com/in/mindy-minsu-kim/) in Wei-Chung Lee's lab at Harvard Medical School. A paper describing the dataset is currently in preparation.
This repository contains:
- A python package for interacting with the connectome data (see the folder [`banc/`](banc), and installation instructions below).
- The `banc` package is a fork on the `fanc` (Female Adult Nerve Cord) package, which can be found at the [upstream repository](https://github.com/htem/FANC_auto_recon). Note that to make it easier to synchronize new features in `banc` and `fanc` packages, the folder `banc/` in this repo is a link to the folder `fanc/` – but files in this repo's version of the `fanc/` folder have been adapted for use with the BANC.
- Other information about the dataset and about the community effort to proofread the connectome (see the [wiki](https://github.com/jasper-tms/BANC-fly-connectome/wiki)).
Have any questions? Please [open an issue](https://github.com/jasper-tms/BANC-fly-connectome/issues/new) or contact [Jasper Phelps (jasper.s.phelps@gmail.com)](http://jasper.science).
## Installing and configuring the `banc` python package
### Before you start
As is always the case in python, consider making a virtual environment (using your preference of virtualenv/virtualenvwrapper or conda) before installing.
### Installation option 1: pip install from PyPI
pip install banc
### Installation option 2: pip install directly from GitHub
The code on GitHub will sometimes be slightly more up to date than the version on PyPI
pip install git+https://github.com/jasper-tms/BANC-fly-connectome.git
### Installation option 3: Clone then install
This is the best option if you want to make changes yourself to the code
cd ~/repos # or wherever you keep your repos
git clone https://github.com/jasper-tms/BANC-fly-connectome.git
cd BANC-fly-connectome
pip install -e .
### Troubleshooting
Depending on your Python 3 version and your operating system, you may need to battle some bugs in order to get the `pip install` commands above to succeed.
If you get something that looks like
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
and you're on a Mac, install `brew` (https://brew.sh) if you haven't yet, then use `brew` to install HDF5 with `brew install hdf5`, then put `HDF5_DIR=/opt/homebrew/opt/hdf5` in front of your `pip install` command (e.g. `HDF5_DIR=/opt/homebrew/opt/hdf5 pip install banc`).
If you get an error that contains
Error compiling Cython file:
...
Cython.Compiler.Errors.CompileError: tables/utilsextension.pyx
try to `pip install` the latest version of `tables` from GitHub by running `HDF5_DIR=/opt/homebrew/opt/hdf5 pip install git+https://github.com/PyTables/PyTables`, or alternatively, use conda to install it (`conda install tables`). After you get this package installed successfully, try installing `banc` again.
### Provide credentials
Access to the latest reconstruction of BANC is restricted to authorized users. If you are a member of the BANC community (see [Collaborative community](../../wiki#collaborative-community) on this repo's wiki) and have been granted access, you can generate an API key by visiting [https://global.daf-apis.com/auth/api/v1/create_token](https://global.daf-apis.com/auth/api/v1/create_token) and logging in with your BANC-authorized google account. Copy the key that is displayed, then run the following commands in python to save your key to the appropriate file:
```python
import banc
banc.save_cave_credentials("THE API KEY YOU COPIED")
```
Alternatively, you can manually do what the command above accomplishes, which is to create a text file at `~/.cloudvolume/secrets/cave-secret.json` with these contents:
{
"token": "THE API KEY YOU COPIED",
"brain_and_nerve_cord": "THE API KEY YOU COPIED"
}
You can verify that your API key has been saved successfully by running:
```python
import banc
client = banc.get_caveclient()
```
### Optional installation steps for additional functionality
#### Install Elastix to transform neurons into alignment with the VNC template
The mesh manipulation and coordinate transform code requires `pytransformix`, which is itself a Python wrapper for Elastix. Therefore, Elastix must be installed and its lib and bin paths must be appended to the `LD_LIBRARY_PATH` and `PATH` environment variables. See [`pytransformix` documentation](https://github.com/jasper-tms/pytransformix#installation) for specific instructions.
## Documentation
- First go through [`fanc_python_package_examples.ipynb`](https://github.com/jasper-tms/BANC-fly-connectome/blob/main/example_notebooks/fanc_python_package_examples.ipynb)
- Then check out other notebooks in [`example_notebooks/`](https://github.com/jasper-tms/BANC-fly-connectome/tree/main/example_notebooks)
- Finally you can [browse the code](https://github.com/jasper-tms/BANC-fly-connectome/tree/main/banc), check out modules that have names that interest you, and read the docstrings.
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"description": "# The Brain And Nerve Cord fly connectome\n\nThe BANC (pronounced \"bank\") is the Brain And Nerve Cord, a GridTape-TEM dataset of an adult _Drosophila melanogaster_'s entire central nervous system. This dataset was generated by [Jasper Phelps](http://jasper.science) and [Minsu Kim](https://www.linkedin.com/in/mindy-minsu-kim/) in Wei-Chung Lee's lab at Harvard Medical School. A paper describing the dataset is currently in preparation.\n\nThis repository contains:\n- A python package for interacting with the connectome data (see the folder [`banc/`](banc), and installation instructions below).\n - The `banc` package is a fork on the `fanc` (Female Adult Nerve Cord) package, which can be found at the [upstream repository](https://github.com/htem/FANC_auto_recon). Note that to make it easier to synchronize new features in `banc` and `fanc` packages, the folder `banc/` in this repo is a link to the folder `fanc/` \u2013 but files in this repo's version of the `fanc/` folder have been adapted for use with the BANC.\n- Other information about the dataset and about the community effort to proofread the connectome (see the [wiki](https://github.com/jasper-tms/BANC-fly-connectome/wiki)).\n\nHave any questions? Please [open an issue](https://github.com/jasper-tms/BANC-fly-connectome/issues/new) or contact [Jasper Phelps (jasper.s.phelps@gmail.com)](http://jasper.science).\n\n## Installing and configuring the `banc` python package\n\n### Before you start\n\nAs is always the case in python, consider making a virtual environment (using your preference of virtualenv/virtualenvwrapper or conda) before installing.\n\n### Installation option 1: pip install from PyPI\n\n pip install banc\n\n### Installation option 2: pip install directly from GitHub\nThe code on GitHub will sometimes be slightly more up to date than the version on PyPI\n\n pip install git+https://github.com/jasper-tms/BANC-fly-connectome.git\n\n### Installation option 3: Clone then install\nThis is the best option if you want to make changes yourself to the code\n\n cd ~/repos # or wherever you keep your repos\n git clone https://github.com/jasper-tms/BANC-fly-connectome.git\n cd BANC-fly-connectome\n pip install -e .\n\n### Troubleshooting\nDepending on your Python 3 version and your operating system, you may need to battle some bugs in order to get the `pip install` commands above to succeed.\n\nIf you get something that looks like\n\n .. ERROR:: Could not find a local HDF5 installation.\n You may need to explicitly state where your local HDF5 headers and\n library can be found by setting the ``HDF5_DIR`` environment\n variable or by using the ``--hdf5`` command-line option.\n\nand you're on a Mac, install `brew` (https://brew.sh) if you haven't yet, then use `brew` to install HDF5 with `brew install hdf5`, then put `HDF5_DIR=/opt/homebrew/opt/hdf5` in front of your `pip install` command (e.g. `HDF5_DIR=/opt/homebrew/opt/hdf5 pip install banc`).\n\nIf you get an error that contains\n\n Error compiling Cython file:\n ...\n Cython.Compiler.Errors.CompileError: tables/utilsextension.pyx\n\ntry to `pip install` the latest version of `tables` from GitHub by running `HDF5_DIR=/opt/homebrew/opt/hdf5 pip install git+https://github.com/PyTables/PyTables`, or alternatively, use conda to install it (`conda install tables`). After you get this package installed successfully, try installing `banc` again.\n\n### Provide credentials\n\nAccess to the latest reconstruction of BANC is restricted to authorized users. If you are a member of the BANC community (see [Collaborative community](../../wiki#collaborative-community) on this repo's wiki) and have been granted access, you can generate an API key by visiting [https://global.daf-apis.com/auth/api/v1/create_token](https://global.daf-apis.com/auth/api/v1/create_token) and logging in with your BANC-authorized google account. Copy the key that is displayed, then run the following commands in python to save your key to the appropriate file:\n```python\nimport banc\nbanc.save_cave_credentials(\"THE API KEY YOU COPIED\")\n```\n\nAlternatively, you can manually do what the command above accomplishes, which is to create a text file at `~/.cloudvolume/secrets/cave-secret.json` with these contents:\n\n {\n \"token\": \"THE API KEY YOU COPIED\",\n \"brain_and_nerve_cord\": \"THE API KEY YOU COPIED\"\n }\n\nYou can verify that your API key has been saved successfully by running:\n```python\nimport banc\nclient = banc.get_caveclient()\n```\n\n### Optional installation steps for additional functionality\n\n#### Install Elastix to transform neurons into alignment with the VNC template\nThe mesh manipulation and coordinate transform code requires `pytransformix`, which is itself a Python wrapper for Elastix. Therefore, Elastix must be installed and its lib and bin paths must be appended to the `LD_LIBRARY_PATH` and `PATH` environment variables. See [`pytransformix` documentation](https://github.com/jasper-tms/pytransformix#installation) for specific instructions.\n\n## Documentation\n- First go through [`fanc_python_package_examples.ipynb`](https://github.com/jasper-tms/BANC-fly-connectome/blob/main/example_notebooks/fanc_python_package_examples.ipynb)\n- Then check out other notebooks in [`example_notebooks/`](https://github.com/jasper-tms/BANC-fly-connectome/tree/main/example_notebooks)\n- Finally you can [browse the code](https://github.com/jasper-tms/BANC-fly-connectome/tree/main/banc), check out modules that have names that interest you, and read the docstrings.\n\n\n",
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