This python package is to be used in conjugation with the Fiji plugin WizardofOz(WoZ) to analyze periodic contractions of cortical waves, which travel around blastomeres in an oscillatory fashion.
Download Fiji from Fiji, After download open Fiji and to install the Fiji plugin WizardofOz check the update cite MTrack.
Click Help ▶ Update....
Click the Manage update sites button.
Select the MTrack update site in the list.
Click Close and then click Apply changes.
Restart Fiji.
Launch the plugin with Plugins ▶ WizardofOz ▶ Local Deformation & Intensity Tracking.
In the plugin the Raw image (shown below) and its segmentation image are the inputs. In the plugin we fit circles for computing the local curvature information using the start, center and end point of a 10 μm strip on the cell surface to fit a circle. The strip is then moved by 1 pixel along the segmented cell and a new circle is fitted. This process is repeated till all the points of the cell are covered. The radius of curvature of the 10 μm strip boundaries are averaged. Kymograph of local curvature values around the perimeter over time is produced by plotting the perimeter of the strip over time. Curvature kymographs obtained from local curvature tracking are then exported into this python package (pecowaco) for amplitude, frequency and velocity of wave analysis.
This package can be installed with:
pip install --user pecowaco
If you are building this from the source, clone the repository and install via
git clone https://github.com/MechaBlasto/PeCoWaCo/
cd PeCoWaCo
pip install --user -e .
# or, to install in editable mode AND grab all of the developer tools
# (this is required if you want to contribute code back to pecowaco)
pip install --user -r requirements.txtPipenv allows you to install dependencies in a virtual environment.
# install pipenv if you don't already have it installed
pip install --user pipenv
# clone the repository and sync the dependencies
git clone https://github.com/MechaBlasto/PeCoWaCo/
cd PeCoWaCo
pipenv sync
# make the current package available
pipenv run python setup.py develop
# you can run the example notebooks by starting the jupyter notebook inside the virtual env
pipenv run jupyter notebookAccess the example folder and run the cells.
The WizardofOz plugin can be run using a single channel image or a dual channel image. The segmentation image for both is the same. In the single channel mode curvature, distance and intensity of the membrane is computed, in dual channel mode the intensity along the membrane of the second channel is computed as well. We provide two notebooks for analysis of these two modes.
Oscillation analysis of PIV data is done on Matlab by using PIVlab 2.02 (Thielicke and Eize J. Stamhuis, 2020; Thielicke and Stamhuis, 2010). Post obtaining the PIV we perfrom the Fast Fourier transform on the x and y velocities of individual vectors coming out of the PIV analysis. FFT of the vector velocities over time is performed using Matlab’s fast Fourier transform function. The resulting Fourier transforms are squared to obtain individual power spectra. Squared Fourier transforms in the x and y directions of all vectors are averaged for individual embryos resulting in mean power spectra of individual embryos. The example code provided only performs the FFT of the vectors obtained from PIV but we do not provide the code to do PIV itself.
Notebook 1) In this notebook, the curvature, distance and intensity kymograph output coming from a single channel of WoZ plugin serves as an input. Users can choose the start and the end points along the x and y axis of kymograph to exclude certain regions from further computation. We calculate the root mean square, space resolved FFT along the time axis and a space averaged FFT plot with interactive bokeh plots. All the information is saved as csv files.
Notebook 2) In this notebook, the curvature, distance and intensity kymograph output coming from dual channel mode of WoZ plugin serves as an input. We compute the same quantities as in notebook 1 but in addition now with the intensity kymograph analysis of the second channel included as well.
- Python 3.7 and above.
Under MIT license. See LICENSE.
- Özge Özgüç
- Varun Kapoor [email protected]