diff --git a/src/pinto_lab_to_nwb/widefield/widefield_notes.md b/src/pinto_lab_to_nwb/widefield/widefield_notes.md index e1c9386..656cfeb 100644 --- a/src/pinto_lab_to_nwb/widefield/widefield_notes.md +++ b/src/pinto_lab_to_nwb/widefield/widefield_notes.md @@ -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. @@ -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