معرفی شرکت ها


fanc-fly-2.0.4


Card image cap
تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر
Card image cap
تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر
Card image cap
تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر
Card image cap
تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر
Card image cap
تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

Tools for the Female Adult Nerve Cord Drosophila EM dataset
ویژگی مقدار
سیستم عامل -
نام فایل fanc-fly-2.0.4
نام fanc-fly
نسخه کتابخانه 2.0.4
نگهدارنده []
ایمیل نگهدارنده []
نویسنده Jasper Phelps
ایمیل نویسنده jasper.s.phelps@gmail.com
آدرس صفحه اصلی https://github.com/htem/FANC_auto_recon
آدرس اینترنتی https://pypi.org/project/fanc-fly/
مجوز -
# FANC_auto_recon FANC (pronounced "fancy") is the Female Adult Nerve Cord, a GridTape-TEM dataset of an adult _Drosophila melanogaster_'s ventral nerve cord. The dataset was first published in [Phelps, Hildebrand, Graham et al. 2021 _Cell_](https://www.lee.hms.harvard.edu/phelps-hildebrand-graham-et-al-2021), after which we applied automated methods for reconstructing neurons, synapses, and nuclei to accelerate reconstruction of the ventral nerve cord connectome. This repository contains a python package for interacting with the connectome (see the folder [`fanc`](fanc)) as well as other supporting files. Have any questions? Please [open an issue](https://github.com/htem/FANC_auto_recon/issues/new) or contact [Jasper Phelps (jasper.s.phelps@gmail.com)](https://github.com/jasper-tms). ## Installing and configuring the `fanc` 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 fanc-fly ### 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/htem/FANC_auto_recon.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/htem/FANC_auto_recon.git cd FANC_auto_recon pip install -e . ### Provide credentials Access to the latest reconstruction of FANC is restricted to authorized users. If you are a member of the FANC 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 FANC-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 fanc fanc.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", "fanc_production_mar2021": "THE API KEY YOU COPIED" } You can verify that your API key has been saved successfully by running: ```python import fanc client = fanc.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. #### Provide CATMAID credentials to pull data from CATMAID You can get your CATMAID API key by logging into https://radagast.hms.harvard.edu/catmaidvnc then hovering over "You are [Your Name]" in the top-right corner, then clicking "Get API token". Save your CATMAID API key by running: ```python import fanc fanc.catmaid.save_catmaid_credentials("YOUR CATMAID API KEY") ``` You can verify that your API key has been saved successfully by running: ```python import fanc fanc.catmaid.connect() ``` ## Documentation - First go through [`fanc_python_package_examples.ipynb`](https://github.com/htem/FANC_auto_recon/blob/main/example_notebooks/fanc_python_package_examples.ipynb) - Then check out other notebooks in [`example_notebooks/`](https://github.com/htem/FANC_auto_recon/tree/main/example_notebooks) - Finally you can [browse the code](https://github.com/htem/FANC_auto_recon/tree/main/fanc), check out modules that have names that interest you, and read the docstrings.


نیازمندی

مقدار نام
- numpy
- matplotlib
- cloud-volume
- python-catmaid
- meshparty
- navis
- flybrains
- transformix
- nglui
- pyperclip
- numpyimage
- pandas
- connected-components-3d
- fill-voids
- task-queue
- caveclient
- cloud-files
- urllib3
- trimesh
- pcg-skel


زبان مورد نیاز

مقدار نام
>=3.6 Python


نحوه نصب


نصب پکیج whl fanc-fly-2.0.4:

    pip install fanc-fly-2.0.4.whl


نصب پکیج tar.gz fanc-fly-2.0.4:

    pip install fanc-fly-2.0.4.tar.gz