Upload Data

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• Import video: Path of folder containing videos for analysis. The videos can be nested within folders of folders and the program will recursively find them based on the file extension. You can either click the browse button to select the file or drag and drop your video folder.


• Import trace: Path of csv file containing traces for analysis. Each row should contain a time series. See examples in GitHub for formatting expected by the program.

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Configuration Page

Create a new ".yaml" configuration file or choose an existing/saved “.yaml” configuration file

• Create new configuration: Create a new ".yaml" configuration file to choose the analysis parameters suitable for your needs, clicking the "New Configuration" button will lead you to the next page and all of the analysis parameters will be set to default values.


• Modify existing configuration: Or you can choose the path of an existing/saved “.yaml” configuration file to import. The program will automatically fill in your previous trace and video analysis settings.

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Video Settings

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• Video file: Video file format to analyze. If format does not appear in the drop down menu, select “Other” and type your own format such as (“mp4”, “avi”). See FFMPEG documentation for full list of supported formats
• Video type: Type of video for analysis. Select fluorescent for calcium or voltage transients, and select brightfield for pixel change based contractility analysis.
• Video Acquisition: Select when uManager or pycromanager is used for acquisition. Large videos are split into multiple files, which are automatically combined based on file name and path for analysis.
• Video masking algorithm: Method for detecting the region of interest. None uses all pixels. Mean FFT is recommended for most videos. Dynamic range is best for speed. You may need to empirically find which method works best for your videos.
• Video reference frame: Method for calculating the reference frame for brightfield contractility videos. Auto detects the relaxed state of cardiomyocytes and averages those frames to use as reference. Range allows the user to specify the range of frames to be averaged for reference. Mean averages the entire video; mean should be used only when there are a few beats in the video.
• Reference tolerance: The amplitude of the peak used to define relaxation when “auto” is selected. Noisier signals require higher tolerance.
• Reference frame range: Video frame index range to use as reference frame. You must manually define the frames in which the cardiomyocytes are relaxed.
• Video frame rate: Frame rate of the videos in frames per second or hertz.
• Video max bpm: Maximum beat frequency of cardiomyocytes. Used during mask detection, automatic reference frame calculation, and trace analysis.

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Trace settings

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• Photobleach correction algorithm: Photobleach correction method. “exp” (recommended) fits an exponential decay function through the valley points to calculate the baseline F0. “power” fits a power function that mimics an exponential decay (use if exp fails to converge). “linear” fits a line of best fit. “interpolation” interpolates between valley points in a “connect the dot” fashion.
• Photobleach_min_prominenece: Peak height prominence threshold for valley detection. Higher threshold is better for noisy signals, but too low values could miss valleys.
• Peak_min_prominence: Sampling rate of trace in samples per second or hertz. Same as video frame rate if exists.
• Max bpm: Maximum beat frequency of cardiomyocytes. Used as a parameter for beat detection to ensure peaks detected is not noise.

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Export data

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• Export configuration file: Path to save the configuration file. You must specify the file location holding the parameters that BeatProfiler will use to analyze the videos.
• Export_summary: Summary contains average and standard deviations of metrics over the beats identified in each trace. Metrics are calculated using ΔF/F0 if photobleach correction is applied. Otherwise, raw_trace is used. See full documentation link for description of the metrics exported.
• Export_peak_summary: Peak summary contains metrics extracted from individual peaks. It contains values at the beat level rather than at the video level generated by the “Summary” option.
• Export_raw_trace: Raw trace contains the unnormalized contraction/calcium trace for each video. For brightfield analysis, it is the average difference in pixel intensity amplitude between each frame to the reference frame. For calcium analysis, it is the average pixel intensity of each frame. Each row contains trace of length ‘t’ from each video where ‘t’ is the number of frames in the video.
• Export_df_f0: ΔF/F0 is the difference in intensity and baseline fluorescence divided by the baseline fluorescence. F0, or baseline fluorescence, is calculated as defined in the photobleach correction options. The resulting trace is a normalized baseline corrected version of the raw trace.
• Export_plot_trace: Trace plot saves two plots: the raw trace, and ΔF/F0 (if photobleach correction is selected). The raw trace plots of each trace, peaks identified, valleys detected (used for baseline fitting), and the baseline function. The ΔF/F0 plot saves the normalized baseline corrected trace as well as its peaks and valleys.
• Export_plot_mask: Mask plot saves a binary mask indicating the automatically detected region of interest (if mask method is selected in video settings).
• Export_beat_segments: Beat segments exports single beat segmentations of each trace. The start and end points are automatically identified and each row contains the ΔF/F0 of one single beat.
• Export_path: Path to save all the exported files. You must specify the location that the program will save files. The program will overwrite any existing files.

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Analysis results

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