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Add miniscope interface #8

Merged
merged 5 commits into from
Oct 22, 2024
Merged

Add miniscope interface #8

merged 5 commits into from
Oct 22, 2024

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h-mayorquin
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Should come after #6

As I have been exploring this topic here:

catalystneuro/roiextractors#356

I think that the format at the moment is too heterogeneous. Let's make an interface that works for this conversion so we can move forward with this project. Once we accumulate more examples (working on that) we can propagate this to roiextractors and neuroconv.

@h-mayorquin h-mayorquin self-assigned this Oct 16, 2024
@h-mayorquin h-mayorquin mentioned this pull request Oct 16, 2024
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@h-mayorquin h-mayorquin marked this pull request as ready for review October 21, 2024 15:18
Base automatically changed from add_sleep_behavior_interface to main October 21, 2024 15:23
@h-mayorquin
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This is ready for review now @alessandratrapani

alessandratrapani
alessandratrapani reviewed Oct 22, 2024
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src/cai_lab_to_nwb/zaki_2024/imaginginterface.py Outdated
def __init__(self, folder_path: DirectoryPath):
self.folder_path = Path(folder_path)

miniscope_videos_folder_path = self.folder_path / "Miniscope"
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This may not work with Cai lab data. For FC, Neutral Exposure and Recall session the folder containing miniscope data is "miniscope" (all lower case). For Offline sessions the folder is called "My_V4_Miniscope". I think we should pass directly what you called miniscope_videos_folder_path

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Good point.

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This may not work with Cai lab data. For FC, Neutral Exposure and Recall session the folder containing miniscope data is "miniscope" (all lower case).

So I developed this against the data from this interface but it is good to be aware. This depends on the subject:

Ca_EEG2-1: folder name: Minscope
Ca_EEG3-4: folder name: miniscope

This makes you point stronger though.

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Changed.

alessandratrapani
alessandratrapani reviewed Oct 22, 2024
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src/cai_lab_to_nwb/zaki_2024/imaginginterface.py Outdated
super().__init__(folder_path=folder_path)

self.folder_path = Path(folder_path)
miniscope_folder = Path(folder_path) / "Miniscope"
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Same here

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Changed.

alessandratrapani
alessandratrapani reviewed Oct 22, 2024
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src/cai_lab_to_nwb/zaki_2024/zaki_2024_notes.md
@@ -776,6 +776,8 @@ This is the metadata file in the same directory that the minian videos:
}
```

Something concerning is that the 30FPS does not correspond to the videos. The metadata says 30 FPS but the videos are 60 FPS.

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@alessandratrapani alessandratrapani Oct 22, 2024 •
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I am not sure that the 60FPS reported in the file property is actually correct.

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I think I checked against OpenCV, why are you suspicious?

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@alessandratrapani alessandratrapani Oct 22, 2024 •
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(looking at subject EEG3-4) Because 60fps is a bit unusual for onephoton imaging (higher than the usual 20-30 Hz) + the timestamps are 33 ms apart (even if they are not always regular), that is 30Hz + if you account for 30fps, the time span of the calcium imaging recording is the same of the behavioral recording which would make more sense instead of recording with miniscope just half of the time (as it would be accounting for 60fps)

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Thanks for writing this. Let me take a close look.

alessandratrapani
alessandratrapani reviewed Oct 22, 2024
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src/cai_lab_to_nwb/zaki_2024/imaginginterface.py
timestamps_seconds = timestamps_milliseconds / 1000.0

# Shift when the first timestamp is negative
# TODO: Figure why, I copied from miniscope
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I guess the timestamps refer to the session start time. If this is correct, when shifting all timestamps, we should also shift back the session start time.

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Let's discuss this briefly in the meeting. I copied this from the current miniscope code on the corresponding extension. I would rather fix the timing issues in one go when we are at the synch stage.

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h-mayorquin commented Oct 22, 2024 •
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I checked how the frame rate is in the jsons files that were shared with and that is consistent:

My grep search on the data that I have (click to expand) 
@h-laptop$ pwd
/media/heberto/One Touch/Cai-CN-data-share/Ca_EEG_Experiment
@h-laptop$ grep -r "frameRate" --include="*.json" .
./Ca_EEG3-4/Ca_EEG3-4_Sessions/Ca_EEG3-4_NeutralExposure/2022_09_17/09_23_03/miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Sessions/Ca_EEG3-4_FC/2022_09_19/09_18_41/miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Sessions/Ca_EEG3-4_Recall1/2022_09_20/09_19_43/miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Sessions/Ca_EEG3-4_Recall2/2022_09_21/08_41_45/miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Sessions/Ca_EEG3-4_Recall3/2022_09_22/08_40_12/miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/09_40_40/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/10_10_41/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/10_40_41/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/11_10_42/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/11_40_42/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/12_10_43/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/12_40_43/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/13_10_44/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/13_40_44/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/14_10_45/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/14_40_45/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/15_10_46/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/15_40_46/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/16_10_47/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/16_40_47/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/17_10_48/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/17_40_48/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/18_10_49/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/18_40_49/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/19_10_50/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/19_40_50/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/20_10_51/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/20_40_51/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay1/2022_09_17/21_10_52/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/09_30_07/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/10_00_07/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/10_30_08/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/11_00_08/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/11_30_09/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/12_00_09/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/12_30_10/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/13_00_10/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/13_30_11/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/14_00_11/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/14_30_12/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/15_00_12/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/15_30_13/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/16_00_13/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/16_30_14/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/17_00_14/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/17_30_15/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/18_00_15/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/18_30_16/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/19_00_16/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/19_30_17/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/20_30_18/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/21_00_18/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG3-4/Ca_EEG3-4_Offline/Ca_EEG3-4_OfflineDay2/2022_09_19/20_00_17/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Sessions/Ca_EEG2-1_FC/10_11_24/Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Sessions/Ca_EEG2-1_NeutralExposure/10_43_54_first_attempt/Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Sessions/Ca_EEG2-1_NeutralExposure/10_44_18/Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Sessions/Ca_EEG2-1_Recall1/10_33_20/Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay1/2021_10_12/10_05_57/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay1/2021_10_12/10_08_17/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay1/2021_10_12/10_10_44/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay1/2021_10_12/10_15_50/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay1/2021_10_12/12_07_50/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/09_24_27/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/09_54_27/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/10_24_27/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/10_54_27/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/11_24_26/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/11_54_26/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/12_24_26/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/12_54_26/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/13_24_26/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/13_54_26/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/14_24_25/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/14_54_25/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/15_24_25/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/15_54_25/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/16_24_25/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/16_54_24/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/17_24_24/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/17_54_24/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflineDay2/2021_10_14/18_24_24/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/11_05_22/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/11_35_22/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/12_05_22/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/12_35_22/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/13_05_21/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/13_35_21/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/14_05_21/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/14_35_21/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/15_05_21/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/15_35_21/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/16_05_20/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",
./Ca_EEG2-1/Ca_EEG2-1_Offline/Ca_EEG2-1_OfflinePre/2021_10_10/16_35_20/My_V4_Miniscope/metaData.json:    "frameRate": "30FPS",

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@alessandratrapani I changed the frame rate on the metadata (see previous comment). I can't force timestamps because I only have done those changes for recording interfaces here:

catalystneuro/neuroconv#1091

We should add that feature for neuroconv in imaging interfaces.

@h-mayorquin h-mayorquin merged commit d191ba1 into main Oct 22, 2024
@h-mayorquin h-mayorquin deleted the add_miniscope branch October 22, 2024 19:06
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