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add eye tracking notes
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weiglszonja committed Dec 3, 2023
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14 changes: 13 additions & 1 deletion src/pinto_lab_to_nwb/widefield/widefield_notes.md
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Expand Up @@ -19,6 +19,15 @@ ROI masks and Allen area labels for the binned session image (blue channel):
- `"roi_from_ref_mat_file_path"`: The file path that contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
- `"info_file_path"`: The file path that contains the information about the imaging session (e.g. number of frames, frame rate, etc.).

## Behavioral data structure

### Eye tracking data (Lightning Pose format)

See the example folder structure [here](https://gin.g-node.org/CatalystNeuro/behavior_testing_data/src/master/lightningpose) for the Lightning Pose format.
- `"lightning_pose_csv_file_path"`: The CSV file with the predictions on labeled data (x, y coordinates and confidence)
- `"lightning_pose_original_video_file_path"`: The original video file (.mp4). The number of frames in this video should match the number of rows in the CSV file.
- `"lightning_pose_labeled_video_file_path"`: The video file (.mp4) with the labeled data. (optional)

## Run conversion for a single session

`widefield_convert_sesion.py`: this script defines the function to convert one full session of the conversion.
Expand All @@ -33,7 +42,10 @@ Parameters:
- "`binned_vasculature_mask_file_path`": The file path that contains the contrast based vasculature mask on the downsampled (binned) session image (blue channel).
- "`binned_blue_pca_mask_file_path`": The file path that contains the PCA mask for the blue channel.
- "`binned_violet_pca_mask_file_path`": The file path that contains the PCA mask for the violet channel.
- "`subject_metadata_file_path`": The file path that contains the subject metadata (e.g. subject_id, genotype, etc.).
- "`subject_metadata_file_path`": The optional file path that contains the subject metadata (e.g. subject_id, genotype, etc.).
- "`lightning_pose_csv_file_path`": Path to the .csv file that contains the predictions from Lightning Pose.
- "`lightning_pose_original_video_file_path`": Path to the original video file (.mp4). The number of frames in this video should match the number of rows in the CSV file.
- "`lightning_pose_labeled_video_file_path`": Path to the labeled video file (.mp4). (optional)

### Example usage

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