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FrozenPy

FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.

FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.

Usage

Installation

FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.

pipinstallFrozenPy

Read .out files

Converting .out to .raw.csv, read .raw.csv:

# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')

Detect freezing and average

Detect freezing:

# detect freezingdata_freezing=fp.detect_freezing(data_raw)

This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:

# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')

This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.

Notes

This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.

Future directions

  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)

About

Python module for analyzing freezing behavior by thresholding motion data

Resources

Readme
MIT license
Activity

Stars

1 star

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FrozenPy
FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.
FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.
Usage
Installation
FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.
pipinstallFrozenPy
Read .out files
Converting .out to .raw.csv, read .raw.csv:
# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')
Detect freezing and average
Detect freezing:
# detect freezingdata_freezing=fp.detect_freezing(data_raw)
This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:
# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')
This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.
Notes
This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.
Future directions
  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)
About
Python module for analyzing freezing behavior by thresholding motion data
Resources
Readme
MIT license
Activity
Stars
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Watchers
2 watching
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FrozenPy
FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.
FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.
Usage
Installation
FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.
pipinstallFrozenPy
Read .out files
Converting .out to .raw.csv, read .raw.csv:
# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')
Detect freezing and average
Detect freezing:
# detect freezingdata_freezing=fp.detect_freezing(data_raw)
This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:
# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')
This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.
Notes
This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.
Future directions
  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)
About
Python module for analyzing freezing behavior by thresholding motion data
Resources
Readme
MIT license
Activity
Stars
1 star
Watchers
2 watching
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Report repository
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FrozenPy
FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.
FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.
Usage
Installation
FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.
pipinstallFrozenPy
Read .out files
Converting .out to .raw.csv, read .raw.csv:
# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')
Detect freezing and average
Detect freezing:
# detect freezingdata_freezing=fp.detect_freezing(data_raw)
This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:
# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')
This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.
Notes
This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.
Future directions
  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)
About
Python module for analyzing freezing behavior by thresholding motion data
Resources
Readme
MIT license
Activity
Stars
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FrozenPy
FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.
FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.
Usage
Installation
FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.
pipinstallFrozenPy
Read .out files
Converting .out to .raw.csv, read .raw.csv:
# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')
Detect freezing and average
Detect freezing:
# detect freezingdata_freezing=fp.detect_freezing(data_raw)
This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:
# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')
This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.
Notes
This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.
Future directions
  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)
About
Python module for analyzing freezing behavior by thresholding motion data
Resources
Readme
MIT license
Activity
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Repository files navigation
FrozenPy
FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.
FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.
Usage
Installation
FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.
pipinstallFrozenPy
Read .out files
Converting .out to .raw.csv, read .raw.csv:
# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')
Detect freezing and average
Detect freezing:
# detect freezingdata_freezing=fp.detect_freezing(data_raw)
This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:
# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')
This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.
Notes
This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.
Future directions
  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)
About
Python module for analyzing freezing behavior by thresholding motion data
Resources
Readme
MIT license
Activity
Stars
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Watchers
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FrozenPy
FrozenPy is a small collection of Python functions for detecting freezing behavior and averaging data based on a threshold and experimental parameters, with a particular focus on Pavlovian conditioning paradigms. Freezing is detected by thresholding motion data under a defined value (e.g., 10 a.u.) for a defined minimum length of time (1 sec). It also includes functions for converting .out files generated from MedPC to easier-to-handle .csv files.
FrozenPy is designed so that it is easy to add metadata (group, sex, etc.) and formats data for use with popular plotting (Seaborn) and statistical (Pingouin) packages within Python.
Usage
Installation
FrozenPy can easily be installed via pip. Type the following into your terminal to install FrozenPy.
pipinstallFrozenPy
Read .out files
Converting .out to .raw.csv, read .raw.csv:
# Base directory containing .out filesout_dir='/path/to/your/.out/files'# convert all .out files within dir to .raw.csvfp.read_out(out_dir)
# read .raw.csvdata_raw=fp.read_rawcsv('your_data.raw.csv')
Detect freezing and average
Detect freezing:
# detect freezingdata_freezing=fp.detect_freezing(data_raw)
This is an example for if we wanted to slice and average data with a 3 min baseline, 10s CS, 2s US, 58s ISI, and 5 trials:
# slice datafrz_bl, frz_trials=fp.get_averagedslices(df=data_freezing,
BL=180,
CS=10,
US=2,
Trials=5,
ISI=58,
fs=5,
Behav='Freezing')
This would output two variables: frz_bl which contained the averaged BL data for each subject, and frz_trials which contained CS, US, and ISI data for each subject. These are separated because BL is factorial data whereas Trials are repeated measures.
Notes
This code was developed specifically for the Maren Lab which uses MedPC boxes that measure motion via loadcells, but it should work with any motion data so long as it is in the correct format. If you notice any problems or wish to contribute please don't hesitate to contact me at mictott@gmail.com, open a pull request, or submit an issue.
Future directions
  • take advantage of xarrays (not in the near future)
  • provide visible feedback to allow for threshold adjustments (not in the near future unless needed)
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Python module for analyzing freezing behavior by thresholding motion data
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