Dataset DOI: 10.5061/dryad.gxd2547zg respository

Description of the data and file structure

This dataset describes RubyACR performance in Drosophila melanogaster with 5 different assays. These five assays correspond to the 5 figures in the accompanying paper. In each assay, there is a “Data” folder containing a pickle file(s) with the data and a “Script” folder containing Python Jupyter notebooks that generate the graphs found in the paper. The Python version and libraries used in the Python environment are described in the Pipfile and Pipfile.lock text files.

Figure 1 includes electrophysiological recordings from the larval NMJ motor neurons expressing RubyACR.

Figure 2 includes imaging from Mi1 neurons expressing RubyACR in the adult.

Figure 3 includes walking behavior when RubyACRs are activated in glutamatergic neurons.

Figure 4 includes memory responses when RubyACRs are activated in dopamine neurons in the adult during training.

Figure 5 measures courtship song frequency when RubyACRs are expressed in pIP10.

Files and variables

The following section describes the files found in the “Repo_Main.zip” folder in this repository. There are 5 subfolders within the zip folder specific to each figure in the paper.

Figure_01: Electrophysiological recordings from larval motor neurons

Here are the folders and files found in the Figure_01 subfolder :

Figure_01
├── Data
│   ├── Protocol_488nm_100ms_0.2-4.9V.pckl
│   ├── Protocol_488nm_10ms_0.2-4.9V.pckl
│   ├── Protocol_488nm_1ms_0.2-4.9V.pckl
│   ├── Protocol_488nm_500ms_0.2-4.9V.pckl
│   ├── Protocol_530nm_100ms_0.2-4.9V.pckl
│   ├── Protocol_530nm_10ms_0.2-4.9V.pckl
│   ├── Protocol_530nm_1ms_0.2-4.9V.pckl
│   ├── Protocol_530nm_500ms_0.2-4.9V.pckl
│   ├── Protocol_660nm_100ms_0.2-4.9V.pckl
│   ├── Protocol_660nm_10ms_0.2-4.9V.pckl
│   ├── Protocol_660nm_1ms_0.2-4.9V.pckl
│   └── Protocol_660nm_500ms_0.2-4.9V.pckl
└── Scripts
├── C19_Genotype_Colors.csv
├── C49_Style.mplstyle
├── C61_GraphingResponsesOverTime_PNG_float16_v004.ipynb
├── C61_MeanVoltageChange_PNG_float16_v05.ipynb
├── C61_MeanVoltageResponseStarts_PNG_float16_v05.ipynb
├── C61_MeasureKinetics_PNG_float16_v003.ipynb

In the data folder, there are pickle files containing pandas dataframes for each type of protocol. The name of the folder indicates the light wavelength used to stimulate channelrhodopsin, the duration in ms, and the range in stimulation intensities. For example, “Protocol_488nm_100ms_0.2-4.9V.pckl” indicates the stimulation wavelength was 488 nm, duration was 100 ms, and the intensity used ranged from 0.2 V to 4.9 V to the LED. In the multi-index pandas dataframe within each pickle file, the column labels correspond with time (ms) when individual sample measurements occurred. The columns are labelled with the time (ms). Within the multi-index, the following describes information within each column:

The statistics being measured:

The Scripts subfolder contains Jupyter notebooks. Other files within the Scripts folder are dependencies defining styles and color guides for the graphs. The following table describes the Jupyter notebooks:

Figure_02 includes imaging from Mi1 neurons expressing RubyACR in the adult

Here are the files within the subfolder Figure_02:

Figure_02
├── Data
│   ├── C05_IntensityMeasurements.ods
│   └── Compiled01_02.pckl
└── Scripts
├── C49_Fig3_Graphing_v03.ipynb
├── ccModules3.py
└── pathlibDB.py

The Data folder contains two files. The C05_IntensityMeasurements.ods is a spreadsheet indicating the voltage sent to the LED and corresponding light intensity targeting the sample. The Compiled01_02.pckl file contains a pandas dataframe with the GCaMP6s intensity measurements during testing. The columns record measurements for each time point. The multi-index rows contain the following columns:

The statistics being measured are as follows:

The Scripts subfolder contains the Jupyter notebook, C49_Fig3_Graphing_v03.ipynb used to generate graphs displaying changes in GCaMP intensity over time and per illumination intensity. Other files within the Scripts folder provide functions used in the Jupyter notebook.

Figure_03 includes walking behavior when RubyACRs are activated in glutamatergic neurons.

Here are the files in the subfolder Figure_03:

Figure_03
├── C13_UAS
│   └── 10sProtocol
│       ├── Data
│       │   ├── C13_ForC49_20240929.pckl
│       │   └── C13_MingRGBIntensity.xlsx
│       └── Scripts
│           ├── C49_GraphingGenieTen_v05.ipynb
│           └── C49_Style.mplstyle
└── C18_LexA
└── 10sProtocol
├── Data
│   ├── C13_MingRGBIntensity.xlsx
│   └── C18_ForC49_20241009.pckl
└── Scripts
├── C49_GraphingGenieTen_v06.ipynb
└── C49_Style.mplstyle

Data is divided into subfolders by driver type. Effectors driven by the GAL4 system are in the C12_UAS folder, while tests using the LexA are in the C18_LexA folder. The data subfolders contain the C13_MingRGBIntensity.xlsx spreadsheet containing the illumination intensity measurements (mW / mm²) per percent LED intensity. The pickle files (*.pckl) contain pandas dataframe detailing the walking velocity (mm/s) at each time point in the protocol. The multi-index has the following columns:

Statistics measured in the frame :

Each Scripts subfolder contains a Jupyter notebook, C49_Graphing GenieTen_v05.ipynb, that graphs the change in velocity over time and mean velocity during baseline and testing periods.

Figure_04 includes memory responses when RubyACRs are activated in dopamine neurons in the adult.

The subfolder Figure_04 contains the following:

Figure_04
├── Data
│   └── PI_annotated.csv
└── Scripts
└── C49_Figure_04_v01.ipynb

In the Data subfolder, the PI_annotated.csv contains the preference index for each animal tested. Test1 uses 13 µW/mm² while test 2 refers to 26 µW/mm² red light illumination during the training.

The Scripts subfolder contains the Jupyter notebook, C49_Figure_04_v01.ipynb, that generates graphs comparing preference index after training between genotypes and illumination intensities.

Figure_05 measures courtship song frequency when RubyACRs are expressed in pIP10.

The subfolder Figure_05 contains the following files:

Figure_05
├── Data1_RedOnly
│   ├── Data
│   │   └── C79_Data1.pckl
│   └── Scripts
│       ├── 02_C79Data1_GraphingResponses-v07.ipynb
│       ├── 03_C79Data1_GraphingPercentChange-v02.ipynb
│       ├── C49_IndividualExamples_v03.ipynb
│       ├── C49_Style.mplstyle
└── Data2_RGB
├── Data
│   └── C79_Data2.pckl
└── Scripts
├── 02_C79Data2_GraphingResponses-v09.ipynb
├── 03_C79Data2_GraphingPercentChange-v02.ipynb
├── C49_Style.mplstyle

The subfolder Data1 contains an experiment testing red illumination intensity only while Data2 tests red, green, and blue illumination. Both folders are structured similarly with a Data subfolder containing a pickle (*.pckl) file storing a pandas dataframe containing the data from the experiment. Entries in the dataframe columns indicate the classification for song recorded during the interval : 0 : no song, 1 : ‘pulse’, and 2 : sine song. The columns in the multi-index are as follows:

The Scripts subfolders contain Jupyter notebooks used to generate graphs comparing courtship song between genotypes and at different illumination intensities. The following table describes the output for the jupyter notebooks:

Other files in the Scripts subfolder contain style guides for the graphs in the Jupyter notebook.