neuralib.atlas.ccf.core

class neuralib.atlas.ccf.core.AbstractCCFDir[source]

ANIMAL_001/ (root)
    ├── raw/ (optional)
    ├── zproj/
    │    └── ANIMAL_001_g*_s*_{channel}.tif
    ├── roi/
    │    └── ANIMAL_001_g*_s*_{channel}.roi
    ├── roi_cpose/
    │    └── ANIMAL_001_g*_s*_{channel}.roi
    ├── resize/ (src for the allenccf, if sagittal slice, could be resize_contra and resize_ipsi)
    │    ├── ANIMAL_001_g*_s*_resize.tif
    │    └── processed/
    │           ├── ANIMAL_001_g*_s*_resize_processed.tif
    │           └── transformations/
    │                 ├── ANIMAL_001_g*_s*_resize_processed_transformed.tif
    │                 ├── ANIMAL_001_g*_s*_resize_processed_transform_data.mat
    │                 └── labelled_regions/
    │                       ├── {*channel}_roitable.csv
    │                       └── parsed_data /
    │                             └── parsed_csv_merge.csv
    ├── resize_*_overlap/ (optional, same structure as **resize**, for dual channels labeling)
    │
    └── output_files/ (for generate output fig)

static __new__(cls, root, with_overlap_sources=True, plane_type='coronal', hemisphere_type=None, auto_mkdir=True)[source]

Parameters:

root (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader)
with_overlap_sources (bool)
plane_type (Literal['coronal', 'sagittal', 'transverse'])
hemisphere_type (Literal['ipsi', 'contra', 'both'] | None)
auto_mkdir (bool)

__init__(root, with_overlap_sources=True, plane_type='coronal', hemisphere_type=None, auto_mkdir=True)[source]

Parameters:

root (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader) – Root path (i.e., */ANIMAL_001)
with_overlap_sources (bool) – If there is overlap channel labeling (for dir making).
plane_type (Literal['coronal', 'sagittal', 'transverse']) – {‘coronal’, ‘sagittal’, ‘transverse’}
hemisphere_type (Literal['ipsi', 'contra', 'both'] | None) – {‘ipsi’, ‘contra’, ‘both’}
auto_mkdir (bool) – If auto make folder structure for the pipeline.

slice_name: str = None

abstract glob(glass_id, slice_id, glob_type, hemisphere=None, channel=None)[source]

Parameters:

glass_id (int) – Glass slide number
slice_id (int) – Slice sequencing under a glass slide (i.e., zigzag from upper left -> bottom left ->-> bottom right)
glob_type (Literal['zproj', 'roi', 'roi_cpose', 'resize', 'resize_overlap', 'processed', 'transformation_matrix', 'transformation_img', 'transformation_img_overlap'])
hemisphere (Literal['i', 'c'] | None)
channel (Literal['r', 'g', 'b', 'merge', 'overlap'] | None)

Returns:

Return type:

Path

abstract property resize_folder: Path

property default_iter_dir: Iterable[Path]

property animal: str

property raw_folder: Path

property roi_folder: Path

property cpose_roi_folder: Path

property zproj_folder: Path

property resize_overlap_folder: Path | None

property processed_folder_overlap: Path | None

property transformed_folder_overlap: Path | None

property labelled_roi_folder_overlap: Path | None

property processed_folder: Path

property transformed_folder: Path

property labelled_roi_folder: Path

property parsed_data_folder: Path

property parse_csv: Path

property output_folder: Path

figure_output(*suffix, sep='_')[source]

Return type:: Path

csv_output(*suffix, sep='_')[source]

Return type:: Path

property roi_atlas_output: Path

property roi_atlas_ibl_output: Path

get_slice_id(glass_id, slice_id, hemisphere=None, channel=None)[source]

Parameters:

glass_id (int)
slice_id (int)
hemisphere (Literal['i', 'c'] | None)
channel (Literal['r', 'g', 'b', 'merge', 'overlap'] | None)

Return type:

str

get_transformation_matrix(glass_id, slice_id, plane_type)[source]

Parameters:

glass_id (int)
slice_id (int)
plane_type (Literal['coronal', 'sagittal', 'transverse'])

Return type:

CCFTransMatrix

class neuralib.atlas.ccf.core.CoronalCCFDir[source]

Base folder structure for 2dccf pipeline

property resize_folder: Path

glob(glass_id, slice_id, glob_type, *, hemisphere=None, channel=None)[source]

Parameters:

glass_id (int) – Glass slide number
slice_id (int) – Slice sequencing under a glass slide (i.e., zigzag from upper left -> bottom left ->-> bottom right)
glob_type (Literal['zproj', 'roi', 'roi_cpose', 'resize', 'resize_overlap', 'processed', 'transformation_matrix', 'transformation_img', 'transformation_img_overlap'])
hemisphere (Literal['i', 'c'] | None)
channel (Literal['r', 'g', 'b', 'merge', 'overlap'] | None)

Returns:

Return type:

Path | None

class neuralib.atlas.ccf.core.CoronalCCFOverlapDir[source]

2dccf Folder structure for multiple sources overlap labeling For example: Dual tracing with different fluorescence protein, and tend to see the overlap channel counts

property resize_overlap_folder: Path: for double labeling channel since maximal 2 channels for roi detection, then need extra folder use pseudo-color

property processed_folder_overlap: Path

property transformed_folder_overlap: Path

property labelled_roi_folder_overlap: Path

glob(glass_id, slice_id, glob_type, *, hemisphere=None, channel=None)[source]

Parameters:

glass_id (int) – Glass slide number
slice_id (int) – Slice sequencing under a glass slide (i.e., zigzag from upper left -> bottom left ->-> bottom right)
glob_type (Literal['zproj', 'roi', 'roi_cpose', 'resize', 'resize_overlap', 'processed', 'transformation_matrix', 'transformation_img', 'transformation_img_overlap'])
hemisphere (Literal['i', 'c'] | None)
channel (Literal['r', 'g', 'b', 'merge', 'overlap'] | None)

Returns:

Return type:

Path | None

class neuralib.atlas.ccf.core.SagittalCCFDir[source]

glob(glass_id, slice_id, glob_type, hemisphere=None, channel=None)[source]

Parameters:

glass_id (int) – Glass slide number
slice_id (int) – Slice sequencing under a glass slide (i.e., zigzag from upper left -> bottom left ->-> bottom right)
glob_type (Literal['zproj', 'roi', 'roi_cpose', 'resize', 'resize_overlap', 'processed', 'transformation_matrix', 'transformation_img', 'transformation_img_overlap'])
hemisphere (Literal['i', 'c'] | None)
channel (Literal['r', 'g', 'b', 'merge', 'overlap'] | None)

Returns:

Return type:

Path | None

property resize_folder: Path

class neuralib.atlas.ccf.core.SagittalCCFOverlapDir[source]

property resize_overlap_folder: Path: for double labeling channel since maximal 2 channels for roi detection, then need extra folder use pseudo-color

property processed_folder_overlap: Path

property transformed_folder_overlap: Path

property labelled_roi_folder_overlap: Path

glob(glass_id, slice_id, glob_type, *, hemisphere=None, channel=None)[source]

Parameters:

glass_id (int) – Glass slide number
slice_id (int) – Slice sequencing under a glass slide (i.e., zigzag from upper left -> bottom left ->-> bottom right)
glob_type (Literal['zproj', 'roi', 'roi_cpose', 'resize', 'resize_overlap', 'processed', 'transformation_matrix', 'transformation_img', 'transformation_img_overlap'])
hemisphere (Literal['i', 'c'] | None)
channel (Literal['r', 'g', 'b', 'merge', 'overlap'] | None)

Returns:

Return type:

Path | None

class neuralib.atlas.ccf.core.CCFTransMatrix[source]

slice_id: str

matrix: MatMatrix

plane_type: Literal['coronal', 'sagittal', 'transverse']

resolution: int

property slice_index: int

__init__(slice_id, matrix, plane_type, *, resolution=10)

Method generated by attrs for class CCFTransMatrix.

Parameters:

slice_id (str)
matrix (MatMatrix)
plane_type (Literal['coronal', 'sagittal', 'transverse'])
resolution (int)

Return type:

None

property delta_xy: tuple[int, int]: map delta value to xy slice view

get_slice_plane()[source]

Return type:: SlicePlane

matrix_info(to_polars=True)[source]

Parameters:: to_polars (bool)
Return type:: dict[str, Any] | DataFrame

neuralib.atlas.ccf.core.load_transform_matrix(filepath, plane_type, resolution=10, default_name='test')[source]

matrix for image transformation

Parameters:

filepath (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader) – transformation matrix .mat file
plane_type (Literal['coronal', 'sagittal', 'transverse']) – PLANE_TYPE {‘coronal’, ‘sagittal’, ‘transverse’}
resolution (int) – atlas resolution
default_name (str) – name of the CCFTransMatrix

Returns:

CCFTransMatrix

Return type:

CCFTransMatrix