ndx-miniscope NWB扩展

这是一个Neurodata扩展（NDX）用于Neurodata Without Borders（NWB）2.0 Miniscope采集数据。

Miniscope扩展了Device核心NWB神经数据类型，包括Miniscope的附加元数据。根据采集软件的版本，数据结构可能相当不同。

Miniscope V4格式

软件记录的数据保存在类似以下的文件夹结构中

    C6-J588_Disc5/ (main folder)
    ├── 15_03_28/ (subfolder corresponding to the recording time)
    │   ├── Miniscope/ (subfolder containing the microscope video stream)
    │   │   ├── 0.avi (microscope video)
    │   │   ├── metaData.json (metadata for the microscope device)
    │   │   └── timeStamps.csv (timing of this video stream)
    │   ├── BehavCam_2/ (subfolder containing the behavioral video stream)
    │   │   ├── 0.avi (bevavioral video)
    │   │   ├── metaData.json (metadata for the behavioral camera)
    │   │   └── timeStamps.csv (timing of this video stream)
    │   └── metaData.json (metadata for the recording, such as the start time)
    ├── 15_06_28/
    │   ├── Miniscope/
    │   ├── BehavCam_2/
    │   └── metaData.json
    └── 15_12_28/

Miniscope V3格式

Miniscope V3采集软件通常输出以下文件

• msCam[##].avi
• behavCam[##].avi
• timestamp.dat
• settings_and_notes.dat

python

安装

获取最新发布版

pip install ndx-miniscope

安装最新版

git clone https://github.com/catalystneuro/ndx-miniscope.git
cd ndx-miniscope
pip install -e .

以下代码演示了如何使用此扩展将Miniscope采集数据转换为NWB。

用法

from datetime import datetime
from dateutil.tz import tzlocal
import glob
import os
from pynwb import NWBFile, NWBHDF5IO
from pynwb.image import ImageSeries
from natsort import natsorted

from ndx_miniscope.utils import (
    add_miniscope_device,
    get_starting_frames,
    get_timestamps,
    read_miniscope_config,
    read_notes,
)

# The main folder that contains subfolders with the Miniscope data
folder_path = "C6-J588_Disc5/"

# Create the NWBFile
session_start_time = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
nwbfile = NWBFile(
    session_description="session_description",
    identifier="identifier",
    session_start_time=session_start_time,
)

# Load the miscroscope settings
miniscope_folder_path = "C6-J588_Disc5/15_03_28/Miniscope/"
miniscope_metadata = read_miniscope_config(folder_path=miniscope_folder_path)
# Create the Miniscope device with the microscope metadata and add it to NWB
add_miniscope_device(nwbfile=nwbfile, device_metadata=miniscope_metadata)

# Load the behavioral camera settings
behavcam_folder_path = "C6-J588_Disc5/15_03_28/BehavCam_2/"
behavcam_metadata = read_miniscope_config(folder_path=behavcam_folder_path)
# Create the Miniscope device with the behavioral camera metadata and add it to NWB
add_miniscope_device(nwbfile=nwbfile, device_metadata=behavcam_metadata)

# Loading the timestamps
behavcam_timestamps = get_timestamps(folder_path=folder_path, file_pattern="BehavCam*/timeStamps.csv")
# Load the starting frames of the video files
# Note this function requires to have `cv2` installed
starting_frames = get_starting_frames(folder_path=folder_path, video_file_pattern="*/BehavCam*/*.avi")


# Legacy usage for Miniscope V3

ms_files = natsorted(glob(os.path.join(folder_path, 'msCam*.avi')))
nwbfile.add_acquisition(
    ImageSeries(
        name='OnePhotonSeries',  # this is not recommended since pynwb has native OnePhotonSeries
        format='external',
        external_file=[os.path.split(x)[1] for x in ms_files],
        timestamps=get_timestamps(folder_path=folder_path, cam_num=1),
        starting_frame=get_starting_frames(folder_path=folder_path, video_file_pattern="msCam*.avi"),
    )
)

behav_files = natsorted(glob(os.path.join(folder_path, 'behavCam*.avi')))
nwbfile.add_acquisition(
    ImageSeries(
        name='behaviorCam',
        format='external',
        external_file=[os.path.split(x)[1] for x in behav_files],
        timestamps=get_timestamps(folder_path=folder_path, cam_num=2),
        starting_frame=get_starting_frames(folder_path=folder_path, video_file_pattern="behavCam*.avi"),
    )
)

annotations = read_notes(folder_path=folder_path)
if annotations is not None:
    nwbfile.add_acquisition(annotations)


save_path = os.path.join(folder_path, "test_out.nwb")
with NWBHDF5IO(save_path, "w") as io:
    io.write(nwbfile)

# test read
with NWBHDF5IO(save_path, "r") as io:
    nwbfile_in = io.read()

MATLAB

安装

git clone https://github.com/bendichter/ndx-miniscope.git

generateExtension('path/to/ndx-miniscope/spec');

用法

建设中...