aicssegmentation.structure_wrapper package

Submodules

aicssegmentation.structure_wrapper.seg_PCNA_earlyS_midS module

aicssegmentation.structure_wrapper.seg_PCNA_earlyS_midS.Workflow_PCNA_earlyS_midS(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure pcna

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_PCNA_lateS module

aicssegmentation.structure_wrapper.seg_PCNA_lateS.Workflow_PCNA_lateS(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure pcna

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_PCNA_lateS_hole_fill module

aicssegmentation.structure_wrapper.seg_PCNA_lateS_hole_fill.Workflow_PCNA_lateS_hole_fill(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure pcna

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_actb module

aicssegmentation.structure_wrapper.seg_actb.Workflow_actb(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure ACTB

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

fn: filename without extension

aicssegmentation.structure_wrapper.seg_actn1 module

aicssegmentation.structure_wrapper.seg_actn1.Workflow_actn1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure ACTN1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_actn1.Workflow_atcn1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure ACTN1 accounting for typo

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentation.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_atp2a2 module

aicssegmentation.structure_wrapper.seg_atp2a2.Workflow_atp2a2(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure ATP2A2

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_actn2 module

aicssegmentation.structure_wrapper.seg_cardio_actn2.Workflow_cardio_actn2(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio ACTN2

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_atp2a2 module

aicssegmentation.structure_wrapper.seg_cardio_atp2a2.Workflow_cardio_atp2a2(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio ATP2A2

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_fbl module

aicssegmentation.structure_wrapper.seg_cardio_fbl.Workflow_cardio_fbl(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio FBL

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_fbl_100x module

aicssegmentation.structure_wrapper.seg_cardio_fbl_100x.Workflow_cardio_fbl_100x(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio FBL 100x

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_myl7 module

aicssegmentation.structure_wrapper.seg_cardio_myl7.Workflow_cardio_myl7(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio MYL7

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_npm1 module

aicssegmentation.structure_wrapper.seg_cardio_npm1.Workflow_cardio_npm1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio NPM1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_npm1_100x module

aicssegmentation.structure_wrapper.seg_cardio_npm1_100x.Workflow_cardio_npm1_100x(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio NPM1 100x

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_tnni1 module

aicssegmentation.structure_wrapper.seg_cardio_tnni1.Workflow_cardio_tnni1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio TNNI1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cardio_ttn module

aicssegmentation.structure_wrapper.seg_cardio_ttn.Workflow_cardio_ttn(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure Cardio TTN

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_cetn2 module

aicssegmentation.structure_wrapper.seg_cetn2.Workflow_cetn2(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure CETN2

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_ctnnb1 module

aicssegmentation.structure_wrapper.seg_ctnnb1.Workflow_ctnnb1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure CTNNB1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_drug_npm1 module

aicssegmentation.structure_wrapper.seg_drug_npm1.Workflow_drug_npm1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for drug treated NPM1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the

aicssegmentation.structure_wrapper.seg_dsp module

aicssegmentation.structure_wrapper.seg_dsp.Workflow_dsp(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure DSP

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_fbl module

aicssegmentation.structure_wrapper.seg_fbl.Workflow_fbl(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure FBL

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_fbl_labelfree_4dn module

aicssegmentation.structure_wrapper.seg_fbl_labelfree_4dn.Workflow_fbl_labelfree_4dn(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure FBL Labelfree 4dn

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_gja1 module

aicssegmentation.structure_wrapper.seg_gja1.Workflow_gja1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure GJA1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_h2b_interphase module

aicssegmentation.structure_wrapper.seg_h2b_interphase.Workflow_h2b_interphase(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure H2B

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_lamp1 module

aicssegmentation.structure_wrapper.seg_lamp1.Workflow_lamp1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure LAMP1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_lmnb1_interphase module

aicssegmentation.structure_wrapper.seg_lmnb1_interphase.Workflow_lmnb1_interphase(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure LMNB1 interphase

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_lmnb1_mitotic module

aicssegmentation.structure_wrapper.seg_lmnb1_mitotic.Workflow_lmnb1_mitotic(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure LMNB1 mitotic

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_myh10 module

aicssegmentation.structure_wrapper.seg_myh10.Workflow_myh10(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure MYH10

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_npm1 module

aicssegmentation.structure_wrapper.seg_npm1.Workflow_npm1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure NPM1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_npm1_SR module

aicssegmentation.structure_wrapper.seg_npm1_SR.Workflow_npm1_SR(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure NPM1 SR

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_npm_labelfree_4dn module

aicssegmentation.structure_wrapper.seg_npm_labelfree_4dn.Workflow_npm_labelfree_4dn(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure NPM Labelfree 4dn

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_nup153 module

aicssegmentation.structure_wrapper.seg_nup153.Workflow_nup153(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure NUP153

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_polr2a module

aicssegmentation.structure_wrapper.seg_polr2a.Workflow_polr2a(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure polr2a

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_polr2a_blob module

aicssegmentation.structure_wrapper.seg_pxn module

aicssegmentation.structure_wrapper.seg_pxn.Workflow_pxn(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure PXN

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_rab5a module

aicssegmentation.structure_wrapper.seg_rab5a.Workflow_rab5a(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure RAB5A

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_sec61b module

aicssegmentation.structure_wrapper.seg_sec61b.Workflow_sec61b(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure SEC61B

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_sec61b_dual module

aicssegmentation.structure_wrapper.seg_sec61b_dual.Workflow_sec61b_dual(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure SEC61B dual

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_slc25a17 module

aicssegmentation.structure_wrapper.seg_slc25a17.Workflow_slc25a17(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure SLC25A17

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_smc1a module

aicssegmentation.structure_wrapper.seg_smc1a.Workflow_smc1a(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure SMC1A

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_son module

aicssegmentation.structure_wrapper.seg_son.Workflow_son(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure SON

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_st6gal1 module

aicssegmentation.structure_wrapper.seg_st6gal1.Workflow_st6gal1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure ST6GAL1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_template module

aicssegmentation.structure_wrapper.seg_template.Workflow_template(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper tempalte

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_terf2 module

aicssegmentation.structure_wrapper.seg_terf2.Workflow_terf2(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure TERF2

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_tjp1 module

aicssegmentation.structure_wrapper.seg_tjp1.Workflow_tjp1(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure TJP1

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_tomm20 module

aicssegmentation.structure_wrapper.seg_tomm20.Workflow_tomm20(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure TOMM20

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_tuba1b module

aicssegmentation.structure_wrapper.seg_tuba1b.Workflow_tuba1b(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure TUBA1B

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.seg_ubtf module

aicssegmentation.structure_wrapper.seg_ubtf.Workflow_ubtf(struct_img: numpy.ndarray, rescale_ratio: float = -1, output_type: str = 'default', output_path: Union[str, pathlib.Path] = None, fn: Union[str, pathlib.Path] = None, output_func=None)

classic segmentation workflow wrapper for structure UBTF

struct_img: np.ndarray

the 3D image to be segmented

rescale_ratio: float

an optional parameter to allow rescale the image before running the segmentation functions, default is no rescaling

output_type: str

select how to handle output. Currently, four types are supported: 1. default: the result will be saved at output_path whose filename is

original name without extention + “_struct_segmentaiton.tiff”

2. array: the segmentation result will be simply returned as a numpy array

3. array_with_contour: segmentation result will be returned together with

   the contour of the segmentation

4. customize: pass in an extra output_func to do a special save. All the

   intermediate results, names of these results, the output_path, and the original filename (without extension) will be passed in to output_func.

aicssegmentation.structure_wrapper.structure_segmenter module

class aicssegmentation.structure_wrapper.structure_segmenter.StructureSegmenter

Bases: object

process_img(gene: str, image: numpy.array, rescale_ratio=-1, module_path='aicssegmentation.structure_wrapper.seg_') -> (<built-in function array>, <built-in function array>)

Module contents