This python-based library allows to query and further analyze neural circuits based on predicted synaptic partners and segmented neurons in volumetric Electron-Microscopy datasets of brain tissue.
- Hardware requirements
- No special hardware requirements - standard computer with enough RAM (~ 8 GB, of course: more is always better).
- Software requirements
- Software has been tested on Linux (Ubuntu 16.04)
from source (creating a conda env is optional, but recommended). Installation takes ~ 3 minutes.
- Clone this repository.
- In a terminal:
conda create -n <conda_env_name> python=3.6
source activate <conda_env_name>
cd synfulcircuit
pip install -r requirements.txt
python setup.py installSee this jupyter notebook as an example of how to use this repository to interact with predicted synapses in the FAFB dataset (also see next section).
In the FAFB dataset [Zheng et al. 2018], 244M predicted synaptic partners [Buhmann et al. 2019] have been intersected with an automatically generated neuron segmentation [Li et al. 2019]. This library allows to query the combined dataset.
For instance, for a given neuron segment id, all up-and downstream neurons can be retrieved. In this example, the downstream neuron partners of the pink neuron projecting from the lobula (brain area marked in blue, part of the visual pathway) are displayed (using neuroglancer).
You can download the combined dataset (244M predicted synapses mapped onto neuron segments) here.
Info on this file: 20191211_fafbv14_buhmann2019_li20190805.db
- has a size of 15 GB.
- Synapses have been mapped onto Li-segmentation version:
20190805 - Synapses live in the CATMAID and neuroglancer-FAFB world. To align them with the local FAFB raw data version stored at Janelia, you have to subtract 40 from the z-value
See this jupyter notebook for more details. You need to add the path of the downloaded file in the first jupyter cell:
synaptic_predictions_dump_fname ='' # Put here the path to the downloaded fileThe runtime of the entire example notebook is ~2 minutes.
On Windows, we enounter a problem in the jupyter notebook when doing sql-queries (Error: "OperationalError: database is locked"). This seems to be a jupyter-notebook problem, until we solve this problem, please, if you get this error, try to run the code outside a jupyter notebook.
In volumetric EM datasets, neurons need to be identified together with synapses to be able to reconstructed the neural circuit (the Connectome). In this tiny example, detected synaptic partners intersected with a neuron segmentation is used to retrieve the underlying neural circuit:
