Installation¶
ClearMap can be installed in different ways. We recommend installation via Anaconda. The altenative is to install from source on Github.
Installation with Anaconda¶
download Anaconda
Install anaconda for Python 3 for your OS and install it folliwng the installation instructions.
clone ClearMap from git
See Cloning.
create a ClearMap conda enviroment using the clear map environment file
ClearMap.yml
.In a terminal change to the ClearMap root folder and type
$ conda env create -f ClearMap.yml
activate your environment
$ conda activate ClearMap
optionally compile ClearMap modules
See Compilation.
run ClearMap
See Running.
trouble shooting
The above might fail due to newer packages than we used to test our code. In that case you can use the
ClearMap_stable.yml
environment file with frozen package versions that works.
Installation via Github¶
clone ClearMap via git
See Cloning.
install the depencies
See Dependencies.
optionally compile ClearMap modules
See Compilation.
run ClearMap
See Running.
Cloning¶
To clone ClearMap make sure git is installed.
In a terminal change to a folder in which you like to place ClearMap and run
$ cd path/to/clearmap
$ git clone https://github.com/ChristophKirst/ClearMap2.git
Compilation¶
All modules are automatically compiled on their first run via cython.
Note
On first run, compiling the various modules may take up to 5-15 minutes!
To trigger compilaltion of all modules in a single step you run the following in a python console:
>>> import ClearMap.Compile
Running¶
To run ClearMap we recommend using spyder. Spyder will be automatically installed in the ClearMap anaconda environment.
To run an analysis ClearMap provides main scripts in
Scripts
.
In spyder, open one of the scripts in the editor and execute the individual cells by placig the cursor in the cell and use Shift + Enter.
Before running, modify the parameters and filenames to match your data and analysis.
The two main scripts are TubeMap and CellMap .
If you just want to set up the ClearMap functions in a python console run
>>> from ClearMap.Environment import *
Dependencies¶
The list of names of python libraries required by ClearMap can be
found in the environment file ClearMap.yml
.
To satisfy all the dependencies the easiet is create a ClearMap environement
via conda
:
$ conda env create -f ClearMap.yml
Alternatively you can install the python dependencies via pip
and use
$ pip install name
You can also do this via the OS software management, e.g. via apt-get
by
using
$ sudo apt-get name
For exmple, if you’re starting from a fresh Ubuntu install, for instance, here are the steps to complete the installation. Open a terminal window and type the following instructions:
Install pip
$ sudo apt-get update $ sudo apt-get install python-pip
Install spyder
$ sudo apt-get install spyder
Install the necessary libraries
$ sudo -H pip install python-opencv $ sudo -H pip install cython $ sudo -H pip install scikit-image $ ...
Computing Resources¶
The processing with CellMap and TubeMap is best done on local workstations or a cluster.
- The minimal requirements for resonable performance are:
256GB RAM
12 CPUs
24GB VRAM
For our work we used either a Dell Precision T7920 or HP Z840 workstation. Each workstation was equipped with 2 Intel Xeon Gold 6128 3.4G 6C/12T CPUs, 512Gb of 2666MHz DDR4 RAM, 4x1Tb NVMe Class 40 Solid State Drives in a RAID0 array (plus a separate system disk), and an NVIDIA Quadro P6000, 24Gb VRAM video card.
The workstations were operated by Linux Ubuntu 18.04LTS.