sl-shared-assets 1.0.0rc1__py3-none-any.whl

sl_shared_assets/suite2p.py

@@ -0,0 +1,449 @@
+"""This module provides the classes used to store suite2p runtime configuration parameters in .YAML files. This is used
+by the sl-forgery library to configure mesoscope data processing via the suite2p library, both during single-day and
+multiday registration processing."""
+
+from typing import Any
+from dataclasses import field, asdict, dataclass
+
+from ataraxis_data_structures import YamlConfig
+
+
+@dataclass
+class Main:
+    """Stores global settings used to broadly define the suite2p processing configuration."""
+
+    nplanes: int = 3
+    """The number of imaging planes in each TIFF file sequence. For Mesoscope frames, this is the number of individual 
+    ROI boxes drawn over the cranial window."""
+
+    nchannels: int = 1
+    """The number of channels per imaging plane. Typically this is either 1 or 2."""
+
+    functional_chan: int = 1
+    """The channel used for extracting functional ROIs (uses 1-based indexing, e.g., 1 means the first channel)."""
+
+    tau: float = 0.4
+    """The timescale of the sensor, in seconds, used for computing the deconvolution kernel. The kernel is fixed to 
+    have this decay and is not fit to the data. Note, the default value was optimized for GCamp6f animals used in 
+    Weinan's OSM Manuscript."""
+
+    force_sktiff: bool = True
+    """Determines whether to force the use of scikit-image for reading TIFF files. This HAS to be true for our tiff 
+    files, as they are compressed in a way that cannot be read with ScanImage tiff reader."""
+
+    fs: float = 10.0014
+    """The sampling rate per plane in Hertz. This is automatically overwritten using ops.json file generated by our 
+    preprocessing pipeline to match the specific acquisition frequency of the processed dataset."""
+
+    do_bidiphase: bool = False
+    """Determines whether to perform computation of bidirectional phase offset for misaligned line scanning 
+    (applies to two-photon recordings only). The suite2p estimates the bidirectional phase offset from 
+    ‘nimg_init’ frames if this is set to 1 (and ‘bidiphase’ to 0), and then applies this computed offset to all 
+    frames."""
+
+    bidiphase: int = 0
+    """The user-specified bidirectional phase offset for line scanning experiments. If set to any value besides 0, then 
+    this offset is used and applied to all frames in the recording."""
+
+    bidi_corrected: bool = False
+    """Indicates whether bidirectional phase correction has been applied tot he registered dataset."""
+
+    frames_include: int = -1
+    """Determines the number of frames to process, if greater than zero. If negative (-1), the suite2p is configured
+     to process all available frames."""
+
+    multiplane_parallel: bool = False
+    """Determines whether to parallelize plane processing for multiplane data. This requires a properly configured 
+    server to parallelize the computations and will not work on the local machine. Due to how suite2p is used in the 
+    lab, this has to always be set to False."""
+
+    ignore_flyback: list[int] = field(default_factory=list)
+    """The list of plane indices to ignore as flyback planes that typically contain no valid imaging data."""
+
+
+@dataclass
+class FileIO:
+    """Stores I/O settings used to specify input data file locations, formats, and output storage options."""
+
+    fast_disk: list[str] = field(default_factory=list)
+    """Specifies the locations where to store the temporary binary files created during processing. If no directories 
+    are provided here, 'save_path0' is used to store the temporary files."""
+
+    delete_bin: bool = False
+    """Determines whether to delete the binary file created during the cell registration stage (registered cells .bin 
+    file). Since registered cell binaries are used by multi-day registration extension, this need to be False for all 
+    lab recordings."""
+
+    mesoscan: bool = True
+    """Indicates whether the input file is a ScanImage Mesoscope recording. For our data, this is always True and all 
+    other formats are False."""
+
+    bruker: bool = False
+    """Indicates whether the provided TIFF files are single-page BRUKER TIFFs."""
+
+    bruker_bidirectional: bool = False
+    """Specifies whether BRUKER files are bidirectional multiplane recordings."""
+
+    h5py: list[str] = field(default_factory=list)
+    """The list of paths to h5py files that will be used as inputs. If provided, these paths overwrite the 'data_path' 
+    field."""
+
+    h5py_key: str = "data"
+    """The key used to access the data array in an h5py file. This should only be provided if 'h5py' is not set to 
+    an empty list."""
+
+    nwb_file: str = ""
+    """Specifies the path to the NWB file to use as an input."""
+
+    nwb_driver: str = ""
+    """The location or name of the driver for reading the NWB file."""
+
+    nwb_series: str = ""
+    """The name of the TwoPhotonSeries in the NWB file to retrieve data from."""
+
+    save_path0: list[str] = field(default_factory=list)
+    """Lists directory paths where the pipeline results should be saved. Typically, this is defined as a single-item 
+    list that stores the path to the output folder used by the processed session's data."""
+
+    save_folder: list[str] = field(default_factory=list)
+    """Lists folder names under which the results should be stored. If this is not provided, the pipeline defaults to 
+    using 'suite2p' as the root folder, created under the path specified by save_path0."""
+
+    look_one_level_down: bool = False
+    """Determines whether to search for TIFF files in the subfolders when searching for Tiff files. If this is True, 
+    the list of evaluated subfolders have to be defined via the 'subfolders' field."""
+
+    subfolders: list[str] = field(default_factory=list)
+    """The list of specific subfolder names to search through for TIFF files."""
+
+    move_bin: bool = False
+    """Determines whether to move the binary file to the save directory after processing, if 'fast_disk' differs from 
+    the 'save_path0'."""
+
+
+@dataclass
+class Output:
+    """Stores I/O settings used to define the output format and organization of the processing results."""
+
+    preclassify: float = 0.5
+    """The probability threshold for pre-classification of cells to use before signal extraction. If this is set to 
+    0.0, then all detected ROIs are kept and signals are computed."""
+
+    save_nwb: bool = False
+    """Determines whether to save the output as an NWB file."""
+
+    save_mat: bool = False
+    """Determines whether to save the results in MATLAB format (e.g., Fall.mat)."""
+
+    combined: bool = True
+    """Determines whether to combine results across planes into a separate 'combined' folder at the end of 
+    processing."""
+
+    aspect: float = 0.666666666
+    """The pixel-to-micron ratio (X:Y) for correctly displaying the image aspect ratio in the GUI (not used in headless
+    processing)."""
+
+    report_time: bool = False
+    """Determines whether to return a dictionary reporting the processing time for each plane."""
+
+
+@dataclass
+class Registration:
+    """Stores rigid registration settings used for correcting motion artifacts between frames."""
+
+    do_registration: bool = True
+    """Determines whether to run the motion registration."""
+
+    align_by_chan: int = 1
+    """The channel to use for alignment (uses 1-based indexing, so 1 means 1st channel and 2 means 2nd channel). If the
+    recording features both a functional and non-functional channels, it may be better to use the non-functional 
+    channel for this purpose."""
+
+    nimg_init: int = 500
+    """The number of frames to use to compute the reference image for registration."""
+
+    batch_size: int = 1000
+    """The number of frames to register simultaneously in each batch. This depends on memory constraints. It is faster 
+    to run the registration if the batch is larger, but it requires more RAM."""
+
+    maxregshift: float = 0.1
+    """The maximum allowed shift during registration, given as a fraction of the frame size, in pixels
+    (e.g., 0.1 indicates 10%)."""
+
+    smooth_sigma: float = 1.15
+    """The standard deviation (in pixels) of the Gaussian used to smooth the phase correlation between the reference
+    image and the current frame."""
+
+    smooth_sigma_time: float = 0.0
+    """The standard deviation (in frames) of the Gaussian used to temporally smooth the data before computing 
+    phase correlation."""
+
+    keep_movie_raw: bool = False
+    """Determines whether to keep the binary file of the raw (non-registered) frames. This is desirable when initially 
+    configuring the suite2p parameters, as it allows visually comparing registered frames to non-registered frames in 
+    the GUI. For well-calibrated runtime, it is advised to have this set to False."""
+
+    two_step_registration: bool = False
+    """Determines whether to perform a two-step registration (initial registration followed by refinement registration).
+    This may be necessary for low signal-to-noise data. This requires 'keep_movie_raw' to be set to True."""
+
+    reg_tif: bool = False
+    """Determines whether to write the registered binary data to TIFF files."""
+
+    reg_tif_chan2: bool = False
+    """Determines whether to generate TIFF files for the registered non-functional (channel 2) data."""
+
+    subpixel: int = 10
+    """The precision for the subpixel registration (1/subpixel steps)."""
+
+    th_badframes: float = 1.0
+    """The threshold for excluding poor-quality frames when performing cropping. Setting this to a smaller value 
+    excludes more frames."""
+
+    norm_frames: bool = True
+    """Determines whether to normalize frames during shift detection to improve registration accuracy."""
+
+    force_refImg: bool = False
+    """Determines whether to force the use of a pre-stored reference image for registration."""
+
+    pad_fft: bool = False
+    """Determines whether to pad the image during the FFT portion of the registration to reduce edge effects."""
+
+
+@dataclass
+class OnePRegistration:
+    """Stores additional pre-registration processing settings used to improve the registration of 1-photon datasets."""
+
+    one_p_reg: bool = False
+    """Determines whether to perform high-pass spatial filtering and tapering to improve one-photon image 
+    registration. For 2-photon datasets, this should be set to False."""
+
+    spatial_hp_reg: int = 42
+    """The window size, in pixels, for spatial high-pass filtering performed before registration."""
+
+    pre_smooth: float = 0.0
+    """The standard deviation for Gaussian smoothing applied before spatial high-pass filtering 
+    (applied only if > 0)."""
+
+    spatial_taper: float = 40.0
+    """The number of pixels to ignore at the image edges to reduce edge artifacts during registration."""
+
+
+@dataclass
+class NonRigid:
+    """Stores non-rigid registration settings used to improve motion registration in complex datasets."""
+
+    nonrigid: bool = True
+    """Determines whether to perform non-rigid registration to correct for local motion and deformation. This is used 
+    for correcting non-uniform motion."""
+
+    block_size: list[int] = field(default_factory=lambda: [128, 128])
+    """The block size, in pixels, for non-rigid registration, defining the dimensions of subregions used in 
+    the correction. It is recommended to keep this size a power of 2 and / or 3 for more efficient FFT computation."""
+
+    snr_thresh: float = 1.2
+    """The signal-to-noise ratio threshold. The phase correlation peak must be this many times higher than the 
+    noise level for the algorithm to accept the block shift and apply it to the output dataset."""
+
+    maxregshiftNR: float = 5.0
+    """The maximum allowed shift, in pixels, for each block relative to the rigid registration shift."""
+
+
+@dataclass
+class ROIDetection:
+    """Stores ROI detection and extraction settings used to identify cells and their activity signals."""
+
+    roidetect: bool = True
+    """Determines whether to perform ROI detection and subsequent signal extraction."""
+
+    sparse_mode: bool = True
+    """Determines whether to use the sparse mode for cell detection, which is well-suited for data with sparse 
+    signals."""
+
+    spatial_scale: int = 0
+    """The optimal spatial scale, in pixels, of the recording. This is used to adjust detection sensitivity. A value of
+    0 means automatic detection based on the recording's spatial scale. Values above 0 are applied in increments of 6 
+    pixels (1 -> 6 pixels, 2-> 12 pixels, etc.)."""
+
+    connected: bool = True
+    """Determines whether to require the detected ROIs to be fully connected regions."""
+
+    threshold_scaling: float = 2.0
+    """The scaling factor for the detection threshold. This determines how distinctly ROIs have to stand out from 
+    background noise to be considered valid."""
+
+    spatial_hp_detect: int = 25
+    """The window size, in pixels, for spatial high-pass filtering applied before neuropil subtraction during 
+    ROI detection."""
+
+    max_overlap: float = 0.75
+    """The maximum allowed fraction of overlapping pixels between ROIs. ROIs that overlap above this threshold are be 
+    discarded."""
+
+    high_pass: int = 100
+    """The window size, in frames, for running mean subtraction over time to remove low-frequency drift."""
+
+    smooth_masks: bool = True
+    """Determines whether to smooth the ROI masks in the final pass of cell detection."""
+
+    max_iterations: int = 50
+    """The maximum number of iterations allowed for cell extraction."""
+
+    nbinned: int = 5000
+    """The maximum number of binned frames to use for ROI detection to speed up processing."""
+
+    denoise: bool = False
+    """Determines whether to denoise the binned movie before cell detection in sparse mode to enhance performance. 
+    If enabled, 'sparse_mode' has to be True."""
+
+
+@dataclass
+class CellposeDetection:
+    """Stores Cellpose algorithm settings used for cell detection."""
+
+    anatomical_only: int = 0
+    """Specifies the Cellpose mode for cell detection:
+        0: Do not use Cellpose. This automatically disables all other fields in this section.
+        1: Detect masks on the max projection divided by the mean image.
+        2: Detect masks on the mean image.
+        3: Detect masks on the enhanced mean image.
+        4: Detect masks on the max projection image.
+    """
+
+    diameter: int = 0
+    """Specifies the diameter, in pixels, of cells to look for. If set to 0, Cellpose estimates the diameter 
+    automatically.."""
+
+    cellprob_threshold: float = 0.0
+    """The threshold for cell detection, used to filter out low-confidence detections."""
+
+    flow_threshold: float = 1.5
+    """The flow threshold, used to control the sensitivity to cell boundaries."""
+
+    spatial_hp_cp: int = 0
+    """The window size, in pixels, for spatial high-pass filtering applied to the image before Cellpose processing."""
+
+    pretrained_model: str = "cyto"
+    """Specifies the pretrained model to use for cell detection. Can be a built-in model name (e.g., 'cyto') or a 
+    path to a custom model."""
+
+
+@dataclass
+class SignalExtraction:
+    """Stores settings used to extract fluorescence signals from ROIs and surrounding neuropil regions."""
+
+    neuropil_extract: bool = True
+    """Determines whether to extract neuropil signals."""
+
+    allow_overlap: bool = False
+    """Determines whether to allow overlap pixels (pixels shared by multiple ROIs) to be used in the signal extraction. 
+    Typically this is set to False to avoid contamination."""
+
+    min_neuropil_pixels: int = 350
+    """The minimum number of pixels required to compute the neuropil signal for each cell."""
+
+    inner_neuropil_radius: int = 2
+    """The number of pixels to keep between the ROI and the surrounding neuropil region to avoid signal bleed-over."""
+
+    lam_percentile: int = 50
+    """The percentile of Lambda within area to ignore when excluding the brightest pixels during neuropil extraction."""
+
+
+@dataclass
+class SpikeDeconvolution:
+    """Stores settings used to deconvolve calcium signals to infer spike trains."""
+
+    spikedetect: bool = True
+    """Determines whether to perform spike deconvolution to convert calcium signals into estimated spike trains."""
+
+    neucoeff: float = 0.7
+    """The neuropil coefficient applied for signal correction before deconvolution."""
+
+    baseline: str = "maximin"
+    """Specifies the method to compute the baseline of each trace. This baseline is then subtracted from each cell. 
+    ‘maximin’ computes a moving baseline by filtering the data with a Gaussian of width 'sig_baseline' * 'fs', and then 
+    minimum filtering with a window of 'win_baseline' * 'fs', and then maximum filtering with the same window. 
+    ‘constant’ computes a constant baseline by filtering with a Gaussian of width 'sig_baseline' * 'fs' and then taking 
+    the minimum value of this filtered trace. ‘constant_percentile’ computes a constant baseline by taking the 
+    'prctile_baseline' percentile of the trace."""
+
+    win_baseline: float = 60.0
+    """The time window, in seconds, over which to compute the baseline filter."""
+
+    sig_baseline: float = 10.0
+    """The standard deviation, in seconds, of the Gaussian filter applied to smooth the baseline signal."""
+
+    prctile_baseline: float = 8.0
+    """The percentile used to determine the baseline level of each trace (typically a low percentile reflecting 
+    minimal activity)."""
+
+
+@dataclass
+class Classification:
+    """Stores settings used to classify detected ROIs as real cells or artifacts."""
+
+    soma_crop: bool = True
+    """Determines whether to crop dendritic regions from detected ROIs to focus on the cell body for classification 
+    purposes."""
+
+    use_builtin_classifier: bool = False
+    """Determines whether to use the built-in classifier for cell detection."""
+
+    classifier_path: str = ""
+    """The path to a custom classifier file, if not using the built-in classifier."""
+
+
+@dataclass
+class Channel2:
+    """Stores settings for processing the second channel in multichannel datasets."""
+
+    chan2_thres: float = 0.65
+    """The threshold for considering an ROI registered in one channel as detected in the second channel."""
+
+
+@dataclass
+class Suite2PConfiguration(YamlConfig):
+    """Stores the user-addressable suite2p configuration parameters, organized into subsections.
+
+    This class is used during processing to instruct suite2p on how to process the data. Specifically, it provides a
+    user-friendly way of specifying all user-addressable parameters through a .YAML file. The sl-forgery library then
+    loads the data from .yaml file and uses it to configure the single-day suite2p pipeline and the multiday suite2p
+    pipeline.
+
+    Notes:
+        The .YAML file uses section names that match the suite2p documentation sections. This way, users can always
+        consult the suite2p documentation for information on the purpose of each field inside every subsection.
+    """
+
+    # Define the instances of each nested settings class as fields
+    main: Main = field(default_factory=Main)
+    file_io: FileIO = field(default_factory=FileIO)
+    output: Output = field(default_factory=Output)
+    registration: Registration = field(default_factory=Registration)
+    one_p_registration: OnePRegistration = field(default_factory=OnePRegistration)
+    non_rigid: NonRigid = field(default_factory=NonRigid)
+    roi_detection: ROIDetection = field(default_factory=ROIDetection)
+    cellpose_detection: CellposeDetection = field(default_factory=CellposeDetection)
+    signal_extraction: SignalExtraction = field(default_factory=SignalExtraction)
+    spike_deconvolution: SpikeDeconvolution = field(default_factory=SpikeDeconvolution)
+    classification: Classification = field(default_factory=Classification)
+    channel2: Channel2 = field(default_factory=Channel2)
+
+    def to_ops(self) -> dict[str, Any]:
+        """Converts the class instance to a dictionary and returns it to caller.
+
+        This dictionary can be passed to suite2p functions either as an 'ops' or 'db' argument to control the
+        processing runtime.
+        """
+
+        # Creates an empty dictionary to store all keys and values
+        combined_ops = {}
+
+        # Iterates through all dataclass fields
+        # noinspection PyTypeChecker
+        for section_name, section in asdict(self).items():
+            # Adds all keys and values from each section to the combined dictionary
+            if isinstance(section, dict):
+                combined_ops.update(section)
+
+        return combined_ops

sl_shared_assets/suite2p.pyi

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+from typing import Any
+from dataclasses import field, dataclass
+
+from _typeshed import Incomplete
+from ataraxis_data_structures import YamlConfig
+
+@dataclass
+class Main:
+    """Stores global settings used to broadly define the suite2p processing configuration."""
+
+    nplanes: int = ...
+    nchannels: int = ...
+    functional_chan: int = ...
+    tau: float = ...
+    force_sktiff: bool = ...
+    fs: float = ...
+    do_bidiphase: bool = ...
+    bidiphase: int = ...
+    bidi_corrected: bool = ...
+    frames_include: int = ...
+    multiplane_parallel: bool = ...
+    ignore_flyback: list[int] = field(default_factory=list)
+
+@dataclass
+class FileIO:
+    """Stores I/O settings used to specify input data file locations, formats, and output storage options."""
+
+    fast_disk: list[str] = field(default_factory=list)
+    delete_bin: bool = ...
+    mesoscan: bool = ...
+    bruker: bool = ...
+    bruker_bidirectional: bool = ...
+    h5py: list[str] = field(default_factory=list)
+    h5py_key: str = ...
+    nwb_file: str = ...
+    nwb_driver: str = ...
+    nwb_series: str = ...
+    save_path0: list[str] = field(default_factory=list)
+    save_folder: list[str] = field(default_factory=list)
+    look_one_level_down: bool = ...
+    subfolders: list[str] = field(default_factory=list)
+    move_bin: bool = ...
+
+@dataclass
+class Output:
+    """Stores I/O settings used to define the output format and organization of the processing results."""
+
+    preclassify: float = ...
+    save_nwb: bool = ...
+    save_mat: bool = ...
+    combined: bool = ...
+    aspect: float = ...
+    report_time: bool = ...
+
+@dataclass
+class Registration:
+    """Stores rigid registration settings used for correcting motion artifacts between frames."""
+
+    do_registration: bool = ...
+    align_by_chan: int = ...
+    nimg_init: int = ...
+    batch_size: int = ...
+    maxregshift: float = ...
+    smooth_sigma: float = ...
+    smooth_sigma_time: float = ...
+    keep_movie_raw: bool = ...
+    two_step_registration: bool = ...
+    reg_tif: bool = ...
+    reg_tif_chan2: bool = ...
+    subpixel: int = ...
+    th_badframes: float = ...
+    norm_frames: bool = ...
+    force_refImg: bool = ...
+    pad_fft: bool = ...
+
+@dataclass
+class OnePRegistration:
+    """Stores additional pre-registration processing settings used to improve the registration of 1-photon datasets."""
+
+    one_p_reg: bool = ...
+    spatial_hp_reg: int = ...
+    pre_smooth: float = ...
+    spatial_taper: float = ...
+
+@dataclass
+class NonRigid:
+    """Stores non-rigid registration settings used to improve motion registration in complex datasets."""
+
+    nonrigid: bool = ...
+    block_size: list[int] = field(default_factory=Incomplete)
+    snr_thresh: float = ...
+    maxregshiftNR: float = ...
+
+@dataclass
+class ROIDetection:
+    """Stores ROI detection and extraction settings used to identify cells and their activity signals."""
+
+    roidetect: bool = ...
+    sparse_mode: bool = ...
+    spatial_scale: int = ...
+    connected: bool = ...
+    threshold_scaling: float = ...
+    spatial_hp_detect: int = ...
+    max_overlap: float = ...
+    high_pass: int = ...
+    smooth_masks: bool = ...
+    max_iterations: int = ...
+    nbinned: int = ...
+    denoise: bool = ...
+
+@dataclass
+class CellposeDetection:
+    """Stores Cellpose algorithm settings used for cell detection."""
+
+    anatomical_only: int = ...
+    diameter: int = ...
+    cellprob_threshold: float = ...
+    flow_threshold: float = ...
+    spatial_hp_cp: int = ...
+    pretrained_model: str = ...
+
+@dataclass
+class SignalExtraction:
+    """Stores settings used to extract fluorescence signals from ROIs and surrounding neuropil regions."""
+
+    neuropil_extract: bool = ...
+    allow_overlap: bool = ...
+    min_neuropil_pixels: int = ...
+    inner_neuropil_radius: int = ...
+    lam_percentile: int = ...
+
+@dataclass
+class SpikeDeconvolution:
+    """Stores settings used to deconvolve calcium signals to infer spike trains."""
+
+    spikedetect: bool = ...
+    neucoeff: float = ...
+    baseline: str = ...
+    win_baseline: float = ...
+    sig_baseline: float = ...
+    prctile_baseline: float = ...
+
+@dataclass
+class Classification:
+    """Stores settings used to classify detected ROIs as real cells or artifacts."""
+
+    soma_crop: bool = ...
+    use_builtin_classifier: bool = ...
+    classifier_path: str = ...
+
+@dataclass
+class Channel2:
+    """Stores settings for processing the second channel in multichannel datasets."""
+
+    chan2_thres: float = ...
+
+@dataclass
+class Suite2PConfiguration(YamlConfig):
+    """Stores the user-addressable suite2p configuration parameters, organized into subsections.
+
+    This class is used during processing to instruct suite2p on how to process the data. Specifically, it provides a
+    user-friendly way of specifying all user-addressable parameters through a .YAML file. The sl-forgery library then
+    loads the data from .yaml file and uses it to configure the single-day suite2p pipeline and the multiday suite2p
+    pipeline.
+
+    Notes:
+        The .YAML file uses section names that match the suite2p documentation sections. This way, users can always
+        consult the suite2p documentation for information on the purpose of each field inside every subsection.
+    """
+
+    main: Main = field(default_factory=Main)
+    file_io: FileIO = field(default_factory=FileIO)
+    output: Output = field(default_factory=Output)
+    registration: Registration = field(default_factory=Registration)
+    one_p_registration: OnePRegistration = field(default_factory=OnePRegistration)
+    non_rigid: NonRigid = field(default_factory=NonRigid)
+    roi_detection: ROIDetection = field(default_factory=ROIDetection)
+    cellpose_detection: CellposeDetection = field(default_factory=CellposeDetection)
+    signal_extraction: SignalExtraction = field(default_factory=SignalExtraction)
+    spike_deconvolution: SpikeDeconvolution = field(default_factory=SpikeDeconvolution)
+    classification: Classification = field(default_factory=Classification)
+    channel2: Channel2 = field(default_factory=Channel2)
+    def to_ops(self) -> dict[str, Any]:
+        """Converts the class instance to a dictionary and returns it to caller.
+
+        This dictionary can be passed to suite2p functions either as an 'ops' or 'db' argument to control the
+        processing runtime.
+        """