PURPOSE OF THE PROJECT: Investigate thrombolysis in porcine and human clots in response to plasma, recombinant tissue-plasminogen activatory (rt-PA), or rt-PA with Definity and ultrasound (US). These experiments helped elucidate the differences in thrombolysis between human and porcine clots. 



ORGANIZATIONAL STRUCTURE: Each .zip file includes the raw data from one 30-min experiment. There is a "*.mat" file with all variables within the MATLAB workspace at the end of the experiment (so not all variables are necessary for data analysis). The relevant variables (i.e. used during data analysis) are:
	'tvec' - Time vector associated with the data collection
	'sSize' - Spatially averaged size of the suture (w/ standard deviation)
	'nsample' & 'nFs' - number of samples & sampling frequency (pulled from PC Oscilloscope)
	'PICK_Scale' - [V/div] scale on scope for the channel where the Picker (passive cavitation detector, described below) is attached
	'picnum' - # of bin files

Non-ultrasound experiments contain 30 "*.bin" files containing the entirety of the microscope images. Ultrasound experiments contain 23 "*.bin" files containing the microscope images as well as 23 "PICK*.bin" files that contain the passively recorded ultrasound emissions. 



METHODOLOGY/PROTOCOL

DATA COLLECTION: Please refer to the manuscript for information on experimental set-up and the experimental groups within this experiment. 

	Images: Images were collected in MATLAB 2012b with the aid of the Image Acquisition toolbox, using a Regita-2000 R charge-coupled device (CCD) camera. 
	Key commands:
		imaqreset; % resets image acquisition memory
		vid = videoinput('qimaging',1,'MONO8_800x600'); % initiated the camera
		frame = getsnapshot(vid); % acquires image from the camera
	    fid = fopen('*.bin', 'a+'); %Open/create *.bin file with user specified name
        fwrite(fid, frame, 'uint8'); %Writes the image to *bin file
        
	Ultrasound emission data: US emissions were collected in MATLAB 2012b with the aid of the Instrument control toolbox. US was turned on and off via commands through an Agilent 33250A function generator. The passive cavitation detector used to detect US emissions was the Picker Roentgen GmbH 595516C single-element long-focus 2.25-MHz transducer and the signal was low-pass filtered and boosted by a wide-band low-noise amplifier prior to digitization using a Pico Technologies 4227 PicoScope PC oscilloscope. . 
	Key commands:
		agilent_interface = serial('com3','BaudRate',9600); 
		fopen(agilent_interface);
		* See https://www.mathworks.com/products/instrument/supported/keysight.html for more information on controlling Agilent instruments using MATLAB
		[handle nsample nFs] = picoStart(Ch1_INIT, Ch2_INIT, Ch1_Scale, Ch2_Scale, Ch1_COUP, Ch2_COUP, Trig_Chan, trigThresh, Fs, dT); % Defines the initializiation (on or off), scale, and coupling for channel 1 & 2, the trigger channel, trigger threshhold, sampling frequency, and length of the time window for the Picoscope. 
		[wfmA wfmB] = picoGetWfmAB2(handle, Ch1_Scale, Ch2_Scale, nsample, nFs); % Acquires waveforms
		picoStop(handle); % Stops picoscope. 
		* See https://www.picotech.com/support/forum71.html for more information on using a Pico Technologies PC Oscilloscope with MATLAB. 
		
		
DATA ANALYSIS: Please refer to the manuscript for information on data analysis and results. 

	Images: Images were opened using MATLAB (mainly 2012b, but also versions up to 2014a) and the edge was detected using MATLAB functions. Detected clot width was verified visually following the completion of the routine and adjusted in a few cases to correct algorithmic errors (<10% of experimental runs [across all data sets]). 
	Key commands:
		fopen(fid), fread(fid); % used to open and read the *.bin files 
		BW = edge(tframe, 'sobel', SobelThres); % finds the edges 
		imagesc(tframe,[0 256]); % images are displayed using imagesc as edges are detected to confirm that edges were properly detected
		
	Ultrasound emission data: US emission data was opened using MATLAB (2012b) and the power spectra of the data was calculated. The energy within UH energy bands between 250 kHz and 1 MHz were summed over a 2-kHz bandwidth centered around each UH frequency. 
	Key commands: 
		fopen(fid), fread(fid); % used to open and read the *.bin files 
		fft(signal); % produces the Fast Fourier Transform on the signal.