Nanoarchitectural ANalysis and Organization (NANO)

Compiling

Prerequisits

Project build is managed using the cmake utility, and requires ITK as a dependency. Make sure both these pre-requisits are satisfied before you start to build this repository. All the instructions below are for a *nix based operating systems. We now list step-by-step process to copy, compile and then run this programme.

Clone this repository

As a first step clone this repo to you local machine as follows.

$ git clone git@github.com:murailab/NANO.git

Prepare for Build

As explained above compilation of this project is handled using cmake. To start the build create a build directory inside the downloaded repository

$ cd NANO
$ mkdir cmake-build

Point the ITK_DIR variable in CMakeLists.txt to appropriate location based on your ITK install. If you installed ITK 5.3 to its default location, then you can set ITK_DIR to something as follows.

$ sed -i '8s/.*/set(ITK_DIR \/usr\/local\/lib\/ITK\/lib\/cmake\/ITK-5.3)/' CMakeLists.txt

Make sure to adjust the path above based on your ITK install location.

Generate Makefiles

Generate the required makefiles using cmake.

$ cd cmake-build
$ cmake ..

Compile

Finally, compile the project using the make utility.

$ make -j 4

Depending on the number of cores available to you, instead of 4 you may use a higher number for faster compilation.

Once you complete the build process, an executable called nano should be generated in the cmake-build folder. This is a commandline utility and the main entry point for running various computational pipelines used in [1]. The examples section below demonstrates how to perform some of the computations.

Usage

Tools For Astrocyte Analysis:

$ nano -input <input_file_path> <-tool, -module n>  -mode 0

Options::

 -input
	 path to input file
 -output
	 path to output file
 -tool
	  If present  will run tool modes instead of submodules
 -module
	 -module 0 : Computation related to distances  
	 -module 0 -mode 0 : compute inter-psd distances along astrocytic volume
	 -module 0 -mode 1 : compute distance from mitochondria to the astrocytic surface and beyond
 -tool -mode n
	 Stand alone scripts/tools modes. Following tools are available:
	 -tool -mode 0 : Resample input image to isotropic grid (default)

Examples

Resample astrocyte volume to an isotropic grid

nano -tool -mode 0 -input <input_file_path>

Distance from mitochondria to astrocyte surface and outside

nano -module 0 -mode 0 -input <input_folder_path>

This step assumes that input_folder_path contains 3D image stacks astrocyte.tif containing the segmented astrocyte and mito.tif containing all the mitochondria inside the astrocyte.

Table of various distance metrics for PSD regions

nano -module 0 -mode 1 <input_folder_path>

Make sure you have already generated various distance function before running this step. (See step above)

Citation

If you use any parts of this code, pleas consider citing the associated paper [1]

References

[1] Salmon, Christopher K., et al. "Organizing Principles of Astrocytic Nanoarchitecture in the Mouse Cerebral Cortex." Current Biology (2023).