leechem: Python code for the Leech SBEM Datasets - ReadMe

1. Introduction

The leechem repository provides python code to retrieve, visualize and analyze data from serial-block face electron microscopy (SBEM) as well as Voltage Sensitive Dye (VSD) Imaging data as published in "Anatomy and activity patterns in a multifunctional motor neuron and its surrounding circuits" by Ashaber, Tomina, Kassraian et al., 2021 - DOI: 10.7554/eLife.61881

• The SBEMDB Database: Contains SBEM reconstruction of the canonical ganglion 10 from the leech with reconstructions of the neurites and synapses of the ganglion. The focus has in particular been the reconstruction of presynaptic projections to neuron DE-3R (tree id 444 in the database), an output motor neuron of the circuit.

• The Python code: Accesses the Electron Microscopy (EM) as well as the Voltage Sensitive Dye (VSD) data, allows for visualization and data analysis:

  • Retrieval: Functions defined in the sbemdb module allow for retrieval of the EM reconstructions. The functions defined here allow, for instance, for the retrieval of the coordinates of the neurites and the synapses.

  • Analysis: The jupyter notebook Clustering_synapses runs the clustering analysis. With the coordinates of synapses as an input, the notebook outputs the membership of synapses to clusters based on a hierarchical clustering approach.

  • Visualization: The jupyter notebook Visualization_DE3R provides an example of the visualization of the neurites of the DE-3R motorneuron and synapses of its presynaptic partners on its neurites. The jupyter notebook Visualization_Clusters illustrates synaptic clusters and their functional properties.

  There is also a file called demo.py that demonstrates the use of the sbemdb.py module.

2. Installation

Python Packages

To run the python code, the relevant python modules need to be installed. These are listed at the beginning of the scripts, see for instance the following lines in sbemdb.py:

import numpy as np
import sqlite3
import errno
import os

This modules need to be installed before running the code, and can be most conveniently done using pip from the terminal. For an introduction to pip, see here.

3. Code

Python code - A very brief overview

The python code relies mainly on sqlite to retrieve the data from the database. In an SQL environment, the typical process is to create a database object and then a so called cursor to retrieve with sql specific clauses the desired information. For instance:

db = SBEMDB() #creating a database object
c = db.db.cursor() #creating the cursor c
c.execute("select name from sqlite_master where type = 'table';") #using the cursor c with a clause to retrieve all table names
table_names = c.fecthall() #retrieve all results from c
print(table_names) #print results

The code in sbemdb.py has been written, however, in a way that sql specific calls are minimized.

The function nodexyz for instance:

def nodexyz(self, where):
        '''NODEXYZ - Get a map of node positions
        (x, y, z, nid) = NODEXYZ(whereclause) performs a SELECT on the NODES 
        with the given where clause. For instance,
        nnn = db.nodes('tid==444 and typ==6') finds
        all the postsynaptic terminals on tree #444.
        Results X, Y, Z are expressed in um and are corrected for the gapshift.
        ID is node ID'''
        c = self.db.cursor()
        c.execute('select nid, x, y, z from nodes where %s' % where)
        rows = c.fetchall()
       (...)
        return (x, y, z, nid)

allows the user to retrieve the 3D coordinates of a note and its id ("nid") via for instance "nodexyz('tid==444')", while the object oriented code creates a cursor and accesses the database hidden from the user.

The most convenient way to get started with the code might be by way of the "demo.py" program.

4. Contact

This work is meant to contribute to the scientific exchange of neural circuit data and relevant analysis methods. We invite everyone interested to reach out with input or questions. You reach us best by mail via daw@caltech.edu or pegahkf@gmail.com