ecc (easy cell counter)

For more information, read the documentation at https://dspsleeporg.github.io/ecc/.

What is it?

ecc is a small Python program to perform cell detection. It will identify the XYZ position, expression amount, and volume of the targeted cells from 3D mouse brain image. It is based on ilastik, a machine-learning framework to train pixel classifiers.

Installation

System requirements

ecc has been developed and tested on Linux platforms (Ubuntu 16.04 LTS and CentOS 7). The code requires Python 3.7 or later.

To run the program, we recommend at least 8GB of system RAM and four cores of CPUs. No other specific hardware are required.

Install ilastik

ecc uses ilastik to train a pixel classifier. Follow this page to install ilastik. For the best compatibility, it is recomennded to use version 1.3.0 or 1.3.2.

Be sure to remember where you installed ilastik. We will need that path when we run ecc.

Install ecc

ecc uses conda to replicate virtual python environment. If you do not have conda installed in your system, you can download miniconda here.

First, clone the repo:

$ git clone https://github.com/DSPsleeporg/easy_cell_counter.git

Then, go to the directory and create a new conda environment:

$ cd ecc
$ conda env create -f environment.yml

This will create a new conda environment named ecc-env, with Python version 3.7.

Now activate the new environment by:

$ conda activate ecc-env

Then, within the virtual environment, install ecc:

(ecc-env) $ pip install .

With good internet connection, the whole installation should be finished in about 10 minutes.

Now you are ready to use ecc. To check that the installation was successful, launch python interpreter and type the following command:

>>> import ecc
>>> help(ecc)

This will print out the help information about the package.

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To learn how to use ecc, please read the documentation.