Summary of behavioral data is located in BehavioralDataSummary.md.
The simplest way to run the code is to set up an isolated python environment for this project. The code requires Python 3.
$ git clone https://github.com/theunissenlab/zebra-finch-memory-lesions
$ cd zebra-finch-memory-lesions
$ python3 -m venv env
$ source env/bin/activate
(env) $ pip install -e .
(env) $ jupyter laban asterisk indicates file that hasn't been added yet
| Filename | Description |
|---|---|
| Subjects.csv | A list of subjects, subject sex, and experimental group assignment (NCM/HVC/CTRL) |
| ExperimentDates.csv | Lists the date ranges that each subject underwent each stage of the experiment |
| Vocalizers.csv* | A table of vocalizer name and sex |
| Stimuli.csv* | Stimulus file metadata for the stimuli contained in Stimuli.zip |
| Stimuli.zip* | A folder stimuli/ containing all the stimulus WAV files, referenced by Stimuli.csv |
| InjectionProtocols.csv | Describes the various injection protocols used, including lesioning agents, amounts, and coordinates |
| SubjectInjections.csv | Describes which subjects underwent which injection protcols in InjectionProtocols.csv |
| LesionQuantificationSummary.csv | Table with lesion volume in four quadrants in each hemisphere for NCM lesioned subjects |
| LesionQuantification/SUBJECT_NAME.csv | A separate table with the human-annotated lesion size data in saggital slices |
| SubjectSongs.zip | A folder SubjectSongs/ that contains recordings of some male subjects' songs before and after lesion |
| TrialData.csv | The main data table with information about every trial for every subject during all the experimental runs |
Data directory should be placed in the top level of this project (i.e. zebra-finch-memory-lesions/data). Some data files must be generated by code in the scripts/ directory.
| Subject Name | Sex | Treatment | Subject Name | Sex | Treatment | |
|---|---|---|---|---|---|---|
| BluYel2571F | F | Control | GraWhi4040F | F | NCM | |
| RedGra7912M | M | Control | GreBlu5038F | F | NCM | |
| WhiWhi2526M | M | Control | RedHpi0710F | F | NCM | |
| YelPur7906M | M | Control | WhiBlu5805F | F | NCM | |
| XXXOra0037F | F | NCM | ||||
| BluWhi0398F | F | HVC | BlaGre1348M | M | NCM | |
| GraYel7337F | F | HVC | GreBla3404M | M | NCM | |
| BluGre4315M | M | HVC | HpiGre0651M | M | NCM | |
| BluRed8773M | M | HVC | XXXBlu0031M | M | NCM | |
| BluWhi3230M | M | HVC | XXXHpi0038M | M | NCM | |
| GreWhi2703M | M | HVC | ||||
| HpiGre8613M | M | HVC |
This project implements functions for loading behavioral and lesion data for our auditory memory project, as well as code for data analysis.
python -m unittest discover testsCode is run and tested on Python3.9, using requirements listed in requirements.txt (install with pip install -r requirements.txt).
Running the notebooks with Jupyter lab requires a couple extensions. To have interactive plots,
ipympl is required along with the jupyter-matplotlib jupyter extension.
It is possible that the jupyterlab-manager extension is also needed, as well as npm and nodejs (>=10.0)