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Intrinsic Imaging

Data acquisition and stimulation

  • Strategy of Kalatsky and Stryker, Neuron (2003): using periodic stimulation (repetitions) and Fourier analysis to catch weak evoked responses.
  • A flickering moving bar (N.B. straight on the screen, unlike Juavinett et al., 2016 or Zhuang et al., 2017)
  • The protocol keeps on adding data. Stop whenever you are happy with the obtained maps.

Retinotopic maps

Building retinotopic maps using the strategy . From a recording movie that contains Nrepeat repetitions of the flickering bar in one irection:

spectrum = np.fft.fft(movie, axis=0)

# generate power map
power_map = np.abs(spectrum)[Nrepeat,:,:]

#generate phase movie
phase_map = -np.angle(spectrum)[Nrepeat,:,:] % (2.*np.pi)

Segmentation of Visual Areas

The code comes from from a script from Jun Zhuang.

Predicted Output

Material and Methods

[...]

Usage

    1. Start Micromanager
    1. Set up stream to pycromanager in micro-manager
    1. Start physion

Installation steps

1) Install the Camera drivers from the manufacturer

Either from:

  • QCam
  • Thorlabs
  • FLIR
  • ...

2) Install Micromanager

Download micromanager from https://micro-manager.org/ and install it.

3) Set up the camera using the Hardware Configuration Wizard of Micromanager

In the GUI, menu: Devices > Hardware Configuration Wizard

N.B. For Thorlab cameras (06/2023)