Binary Heatmap Image

Generates a binary heatmap image. Processing steps:

Heatmap Generation Iterates through the video frames, performing an Otsu automatic threshold to binarize the frames, then aggregates them using a minimum Z-Projection.
Background Reference Creation: Performs a second iteration over the frames to calculate the Average Z-projection of the raw footage.
Final Composition: Binarizes and inverts the generated average image (using the same method), then adds it mathematically to the binary heatmap to produce the final result.

Interface

Interface image

Expected Output

Expected output image

Input Video

Any videos supported by ffmpeg. This includes most video formats in existence. Notably, one exclusion: AVI videos saved from ImageJ with compression set to "None" (codec rawvideo) will not work.

Open Frame

Opens the first frame of the video as a preview. Can be used to set the ROI in functions that require it. Ignores the file's EXIF rotation data.

Output Image

The path to save the operation's image output. Tiff is the recommended format, although all formats supported by OpenCV imwrite are supported.

Save Output

Choose whether to save the output to the specified output path. If left unchecked, only displays the output.

Start and End frame

Specify the frame number to begin and end the processing.

The selection is inclusive, meaning both the start and end frames will be processed.

Frame numbers are one-indexed (the first frame has a frame number equal to 1).

To process the video all the way to its final frame, enter 0 in the 'End frame' field.

Preview

Shows a preview of the function, using the first 10 frames ahead of the Start frame set by the user.