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--- |
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configs: |
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- config_name: worm_data_short |
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data_files: |
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- split: train |
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path: "worm_data_short.parquet" |
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language: |
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- en |
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license: mit |
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--- |
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**CITATION** |
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[Q. Simeon, L. Venâncio, M. A. Skuhersky, A. Nayebi, E. S. Boyden and G. R. Yang, "Scaling Properties for Artificial Neural Network Models of a Small Nervous System," SoutheastCon 2024, Atlanta, GA, USA, 2024, pp. 516-524, doi: 10.1109/SoutheastCon52093.2024.10500049.](https://ieeexplore.ieee.org/document/10500049) |
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<a href="https://github.com/qsimeon/worm-data-preprocess"> |
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<img src="https://img.shields.io/badge/GitHub-100000?style=for-the-badge&logo=github&logoColor=white" /> |
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</a> |
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**DATASET PROCESSING** |
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worm_data_short.parquet is generated by aggregating the info from 12 neural activity source datasets. |
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Each source dataset is processed as follows: |
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1. **Loading** raw data in various formats (MATLAB files, JSON files, etc.). |
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1. Extracting relevant data fields (neuron IDs, traces, time vectors, etc.). |
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1. Cleaning data |
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1. **Resampling** the data to a common time resolution. - if requested |
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1. **Smoothing** the data using different methods - if requested |
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1. **Normalizing** data |
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1. Creating dictionaries to map neuron indices to neuron IDs and vice versa. |
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1. Saving the preprocessed data into a standardized format. |
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**DATASET CONFIG** |
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This dataset was preprocessed with the following hyperparameters. To modify or reproduce the dataset with new settings, refer to the [source code](https://github.com/qsimeon/worm-data-preprocess). |
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- `resample_dt`: `0.333` — Time step for resampling |
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- `interpolate`: `"linear"` — Method used to fill missing data |
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- `smooth`: |
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- `method`: `"moving"` — Smoothing algorithm (`none`, `gaussian`, `exponential`, `moving`) |
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- `alpha`: `0.5` — Exponential smoothing factor |
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- `sigma`: `5` — Gaussian kernel width |
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- `window_size`: `15` — Window size for moving average |
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- `norm_transform`: `"standard"` — Type of normalization (`standard` or `causal`) |
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**FIGURE** |
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Compiled neural activity dataset from GCaMP calcium imaging of _C. elegans_ from multiple experimental sources, standardized to a common sampling rate and organization format. |
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**EXAMPLE USAGE** |
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To use this dataset, you may load or download it using the [`datasets`](https://huggingface.co/docs/datasets/en/loading) and [`huggingface_hub`](https://huggingface.co/docs/huggingface_hub/en/guides/download) libraries, respectively. |
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See this notebook on an example of how to download the dataset and begin working with the data. |
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<a target="_blank" href="https://colab.research.google.com/drive/1z7h2gGuWhupRtjpYc7IHFD4rJ4kIsyuD#scrollTo=ZiZXMRc931oy"> |
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<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/> |
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</a> |
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Google Colab notebook example of loading this dataset and then plotting a few samples of calcium data. |
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**ORIGINAL DATA FILES** |
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We provide a [Dropbox link](https://www.dropbox.com/scl/fi/vfygz1twi1jg62cfssc0w/opensource_data.zip?rlkey=qa4vpwcoza3k9v5o2watwblth&dl=0) to download the original data that we obtained from various sources, including publicly available and unpublished data shared with us by researchers. The `raw_data_file` in the dataset table references these files. |
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If you'd like to preprocess the data from scratch using different preprocessing settings or datasets, you may do so using the code in the [worm-data-preprocess](https://github.com/qsimeon/worm-data-preprocess) repo. |
