Detect_MedianThresh.py setect objects in video and save the dimensions of bounding boxes using background subtraction
findZ.py loads images from a directory and uses keyboard to adjust reconstruction Z and save reco image with Z value embedded in file name
findZ_histogram findZ.py program with a histogram plot of pixel intensity for reconstructed image
findZ_line findZ.py program with a plot of pixel intensity of the reconstructed image across the middle row
holoVideoReco.py loads an mp4 videos, user selects frame, crops image, adjusts reconstruction Z, and saves raw and reco images
detect.py reads a video frame-by-frame, detects objects and saves location, area, and aspect ratio to a file
HSV_colorSpace.py examples of how represent and manipulate images as numpy arrays and explore HSV color space
examineReco.py demonstrates how reconstruction works
phaseAbbScan.py visualizes the phase abberition calculations over a range of z values, to demonstrate how reconstruction works
bouncingSquare.py demonstrates creating and manipulating image numpy arrays using a bouncing red square as an example
streamRecoLine.py interactive holographic reconstruction with Tkinter interface with line contrast display
testStreamingVideo.py find out the address of the microscope (as external USB camera)
HW6Task3_helper.py assigns the IDs of the closest objects in the previous frame to the objects in the current frame (used for tracking)
detectBlur.py detect program with blur to try and prevent an object from having multiple bounding boxes
USB_CAM.docx how to convert Raspberry Pi into a USB camera
renameFiles.py renames files in a directory with an ascending number
keyboard.py changes variables with keyboard while program is running
reco.py performs holographic reconstruction
playChords.py play notes as a chord, arpeggiated, etc. Requires pyGame midi player.note
playNote.py demonstrates playing notes on different midi instruments in the computer using pygame
focusGabor.py autofocus program that run a stack of images through a 0 and 90 deg Gabor Filter and select the image with the highest Gabor value (indicating best focus)
tone_plot.py generates a series of sine waves, plots and sends them out the speaker.
bulk_any_to_mp4.py Convert any video files in a directory into mp4 format.
Code written by Thomas G. Zimmerman, IBM Research-Almaden and Center for Cellular Construction, except Holgraphic Reconstruction Algorithms by Nick Antipac, UC Berkeley and Daniel Elnatan, UCSF. This work is funded by the National Science Foundation (NSF) grant No. DBI-1548297, Center for Cellular Construction. Disclaimer: Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.