CONTRACTIONWAVE (CW) is a free software developed in Python Programming Language that allows the user to visualize, quantify, and analyze cell contractility parameters in a simple and intuitive format. The software enables the user to acquire membrane kinetics data of cell contractility during contraction-relaxation cycles through image capture and a dense optical flow algorithm. Both method and software were developed using multidisciplinary knowledge, which resulted in a robust data extraction protocol.
For more information access: https://sites.icb.ufmg.br/cardiovascularrc/contractionwave/
Contractionwave can be installed from an executable file (3.1 section – for Windows or Ubuntu) or from Anaconda environment installation (3.2 section below – for Windows, Ubuntu, or Mac-OS).
These installations steps can also be found on the program's manual on: https://sites.icb.ufmg.br/cardiovascularrc/contractionwave/
Step 1: The latest stable version compiled executable for Windows and Ubuntu (64-bit) can be downloaded from: The link to the executable file in the Mendeley website is presented below: https://sites.icb.ufmg.br/cardiovascularrc/contractionwave (Choose the Operating System and click on Download)
In Experiment data files click on CONTRACTIONWAVE - Executable file (Windows or Ubuntu) folder and choose the Operating System to download.
Step 2: Unpack the zip file
Step 3: The extracted directory contains a library folder and one executable file (.exe for Windows)
Step 4: Double-click on the CW icon to start the executable file
Wait until the CONTRACTIONWAVE window opens (it might take some time). Then, you can proceed to section 3.3- Quick Start Guide.
Step 1: Download CONTRACTIONWAVE code
a) Access the page https://github.com/marceloqla/ContractionWavePy
b) Click on the "Code" green button on the right hand side of the screen
c) Click on the "Download ZIP" button.
d) Unpack the file and complete the extraction process to a desired target directory.
Step 2: Installation using Anaconda
Follow the instructions for installing Anaconda:
Windows: https://docs.anaconda.com/anaconda/install/windows/
Mac-OS: https://docs.anaconda.com/anaconda/install/mac-os/
Linux: https://docs.anaconda.com/anaconda/install/linux/
After the installation is complete, close the Anaconda dialog box and then go to step II. (no need to register)
Step 3: Open Anaconda Prompt
Windows: Click Start, search, or select Anaconda Prompt from the menu. Mac-OS: Cmd+Space to open Spotlight Search and type “Navigator” to open the program. Ubuntu: Open the Dash by clicking the upper left Ubuntu icon, then type “terminal”.
Please refer to other materials for opening the Terminal in other Operating Systems.
Step 4: Access the directory in which the ZIP file was extracted
To access the ContractionWavePy-master directory follow the instructions below:
Windows: Right mouse click on desired file/folder > Select and click Properties The full path should be under the “Location” tab.
MacOS: the "Finder" application to access the containing folder of the extraction target directory and follow the instructions on: https://www.josharcher.uk/code/find-path-to-folder-on-mac/ Instructions include pressing the "Command ⌘" or "cmd ⌘" and the "i" keyboard keys at the same time AFTER selecting the extraction target directory containing the program. A new window will open and the full path for the directory will be shown in the "General > Where" tab.
Ubuntu: Right mouse click on desired file/folder > Select and click Properties The full path should be under the “Parent folder” tab.
For example, if the full path for the directory is:
"/Users/PC-name/Desktop/ContractionWavePy/"
you should type in the Anaconda Prompt the following command (Example):
cd /Users/PC-name/Desktop/ContractionWavePy-master/
And then press “Enter” to access this folder using the Anaconda Prompt window.
Important: type: "cd " with space before the extracted program folder full path for accessing this folder on the “Anaconda Prompt”.
FAQ
Q: I've been getting: "python: can't open file "ContractionWave.py':[Errno 2]: No such file or directory"
A: Check that you are in the correct directory for running the program. Remember to type: "cd " before the extracted program folder full path for accessing this folder on “Terminal”.
Step 5: Install all dependencies for ContractionWave using Anaconda
Important: Make sure you have a stable internet connection.
ContractionWave dependecies be easily installed by typing the following command on the previously opened Anaconda Prompt window:
Windows:
conda env create -f ContractionWavePy-windows.yml Press “Enter” to start the installation.
Mac-OS:
conda env create -f ContractionWavePy-mac.yml Press “Enter” to start the installation.
Ubuntu:
conda env create -f ContractionWavePy-ubuntu.yml Press “Enter” to start the installation.
Wait until all installations are concluded (it might take some time – 10 to 40 minutes)
Step 6: Executing ContractionWave
I. Open the Anaconda Prompt as instructed in Step 3.
II. Access the Extracted folder by typing the full path for the ContractionWavePy-master directory as instructed in section Step 4.1
III. Activate the Anaconda environment by typing on the previously opened Anaconda Prompt window.
Type in the Anaconda Prompt the following command:
conda activate ContractionWavePy And then press “Enter” to start the environment and then go to step 7.
Important: You should be able to see the Terminal (base) prefix change to (ContractionWavePy)
Step 7: Run the ContractionWave program by typing on the previously opened Anaconda Prompt window
Type in the Anaconda Prompt the following command:
python ContractionWave.py
And then Press “Enter” to start the program. Wait until the ContractionWave window opens (it might take some time). Then, you can proceed to section 3.3- Quick Start Guide.
FAQ
Q: ContractionWave is not opening, what can be done?
A: If for any reasons ContractionWave does not open, try to remove the environment in the Anaconda Prompt
conda env remove -n ContractionWavePy Press “Enter” to remove the environment.
Or try to update Anaconda in the Anaconda Prompt
conda update -n base -c defaults conda Press “Enter” to update Anaconda.
and start again the steps from: II- ContractionWave environment installation with Anaconda Prompt (Should only be executed once)