Data set of "Motile cilia hydrodynamics: Entrainment versus synchronisation when coupling through flow"

We gathered videos of cilia dynamics from already published dataset. For each animal/microorganism we have videos in different formats depending on the source:

- .tiffs  usually in a directory, it is composed by a series of images

- .movie    a format that we use in our lab and that it is combatible with our software in Matlab to tack cilium waveform

- .avi 		

For each video we also have the results of the cilia waveform tracking with our software. The resuts from a single video are all in a Matlab  variable that has the same name of the video but with the extension .clclk_force

for example for the video "filename", the results are in "filename.clclk_force".
In Matlab these can be loaded as force = load('filename.clclk_force','-mat');
For all the videos these can be directly be found in the directory cilium waveforms force files.

You can access this results for example: 

--------------- copy this to Matlab script --------------------
%%%%% go to youdir/cilium waveforms force files/brain/
force = load('15.20.clclk_force','-mat');

%%%% plot the cilium waveform with Matlab
figure();
colors= jet(40);
for jj=1:40;
    color=colors(jj,:);
    plot(force.px2mum*force.points(jj).cilium_x,-force.px2mum*force.points(jj).cilium_y,'color',color);hold on;
end
colorbar()
axis equal

%%%%Then you can access the cilia waveforms using the following commands

force.px2mum; %%%% pixel to micron ratio
force.points(jj).cilium_x; %x-coordinate of the timepoint jj
force.points(jj).cilium_y; %y-coordinate of the timepoint jj (this one are inverted, indeed I put a - in the plot figure)
force.clicked_frames(jj).timestamp;   %%% timepoint jj in seconds
force.approximate_clickrate; %%%% frame rate of the clicking

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---------------------------- Code available on github ----------------------------------------

If you want to recreate such results from the movies you can use the software the Dr. Luigi Feriani developed (and that we used for the paper). This is explained in the Matlab file on github: https://github.com/NicolaPellicciotta/CiliaTracking.

From the cilia waveforms is possible to extract rower potentials. The code for doing that is on Dr. Hamilton github
https://github.com/eawh/RowerCompression. Check the README.md on this link for detailed instructions. 


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Here info about the framerate and pixel to micron ratio for each movie.


filename					px2mu	fps

brain:

atAno5_16000 					0.0543	200 

wtcNo7_40000 					0.107	200

60X_15.20.55					0.086	625

chlamy and quadri:

chlamy_3000					0.26	3000

quadri_gallop					0.26	3000

quadri_trot					0.26	3000

airways:

2.60x_1.5x_T72_i1_BSA_profile_day11		0.065	476
06_28_17_WTVito_500fps_edge_4-Movie_Export-0.	0.065	500

volvox:

all the videos are 				0.41	1000