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Tip revision: 73eee24e387e11c259a3f3fe0bd4e469048b25e6 authored by Daniel A. Wagenaar on 02 December 2020, 17:53:44 UTC
Minor updates ahead of eLife resubmission
Tip revision: 73eee24
# 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.  

- 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 ** that demonstrates the use of the ** module.

## 2. Installation

### Python Packages

To run the python code, the relevant python packages need to be installed. See for instance the following lines in

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 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 "" 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 or

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