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Biomechanics and function of proprioceptors: Python analysis class and functions

Jupyter notebook containing python class and functions for analyzing calcium imaging and cell movement tracking data recorded from the leg of fruit flies.

Brief description of the notebook/class/functions

Manually_selecting_ROI_for_vibration_response_at_individual_z_level.ipynb:

Jupyter notebook containing a class and scripts for manually selecting the ROI for the vibration responses at the individual z level

  • shows the example usage and the actual ROI selection for all the data in the paper.
  • configured to run on the local computer instead of on google colab. Example_ROI_selection

Manually_selecting_the_most_right_and_left_club_dendritic_tips.ipynb:

Jupyter notebook containing a class and scripts for manually selecting the most right and left dendritic tips of the club neurons

  • shows the example usage and the actual tip selection for all the data in the paper.
  • configured to run on the local computer instead of on google colab. Example_dendritic_tip_selection

20210712_python_class_for_preprocessing_two_photon_imaging_data.ipynb:

Python class for preprocessing two-photon imaging data and example usages

  • Read image files recorded by ScanImage and demultiplex the images into green and red channel.

  • Filter images with gaussian filter (of specified kernel size).

  • Subpixel image motion correcion using FFT.

  • Use end-of-the-frame signals for two-photon images and IR high-speed camera images to synchronize the two imaging stream.

  • Make a movie that shows two-photon images (both green and red channel) and IR high-speed camera images simultaneously for quick review.

  • This example Jupyter notebook is set to run on google colab using data on google drive.

  • Parameters in the .yaml files are set for downstairs two-photon microscope.