Microscope_App

Confocal Microscope App

Requirements

• Python 3.6.8
• scopefoundry
• numpy
• pyqt
• qtpy
• h5py
• pyqtgraph
• pillow
• pyserial
• customplotting
• python seabreeze
• pipython (contact manufacturer to get software)

Includes

• OceanOptics Spectrum Measurement
  • Plot spectrometer readout over specified integration time
  • Save single spectrum
  • Continuously save spectrum
• OceanOptics PI Piezo Stage Scan
  • Piezo Stage raster scan taking OceanOptics spectrum at each point
  • XY or YX scans
  • Reverse scans
  • Live update of intensity sums
  • Live spectrometer readout
  • Click and export absolute positions
  • Move Piezo Stage to a clicked point
  • Export intensities image
  • Export intensities array
  • Automatically saves scan data in .pkl file
• PicoHarp Countrate Measurement
  • Measure PicoHarp countrate continuously or over specified integration time
  • Export countrate data
• PicoHarp Histogram Measurement
  • Measure PicoHarp histogram continuously or over specified integration time
  • Export histogram data
• PicoHarp PI Piezo Stage Scan
  • Piezo Stage raster scan taking PicoHarp histogram at each point
  • XY or YX scans
  • Reverse scans
  • Live update of intensity sums
  • Live histogram reading
  • Click and export absolute positions
  • Move Piezo Stage to a clicked point
  • Export intensities image
  • Export intensities array
  • Automatically saves data in .pkl file
• PI Piezo Stage Independent Movement
  • Load file containing absolute positions, produced by stage scan selections or manually formatted
  • Move Piezo Stage to each successive point, pausing for the specified sleep time
• PI Piezo Stage Control
  • Simple interface for relative stage movements up, down, left, and right
  • Specify step size for relative movement
• Particle Selection
  • Load camera image and select magnification
  • Assuming stage is centered on the starting point:
    • Select start point and second point, and move stage to second point
    • Click particles on image and export relative positions
• Particle Spectra Measurement
  • Load relative positions of particles from Particle selection
  • Take a spectrum at each particle
  • Automatically saves each spectrum
• Stepper Motor Control
  • Simple interface for relative stepper motor movements up, down, left, and right
  • Specify step size for relative movement
• PicoHarp Avalanche Photodiode Scan
  • APD raster scan taking PicoHarp histogram at each point
  • XY or YX scans
  • Reverse scans
  • Live update of intensity sums
  • Live histogram reading
  • Export intensities image
  • Export intensities array
  • Automatically saves data in .pkl file

Screenshots

OceanOptics Spectrum Measurement

OceanOptics PI Piezo Stage Scan

PicoHarp Countrate Measurement

PicoHarp Histogram Measurement

PicoHarp PI Piezo Stage Scan

PI Piezo Stage Independent Movement

PI Piezo Stage Control

Particle Selection

(https://github.com/SarthakJariwala/Microscope_App/blob/stepper_motor/Screenshots/Microscope_App_particle_selection2.png)

Particle Spectra Measurement

Stepper Motor Control

PicoHarp Avalanche Photodiode Scan

Installing dependencies from command-line

conda install numpy pyqt qtpy h5py pyqtgraph
conda install -c poehlmann python-seabreeze
pip install git+git://github.com/ScopeFoundry/ScopeFoundry.git
pip install pillow pyserial customplotting==0.1.4.dev0

Run instructions

After setup, you can run the application by double-clicking Microscope_app.py. You can also run it from command-line:

python Microscope_app.py