masks
get_dab_mask(ihc, dab_thr=0.03, object_min_size=1000, hole_min_size=1000, tissue_mask=None, he=None, binary_op=None, r=10)
Computes a mask using otsu thresholding on DAB channel on an immunohistochemistry image.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ihc |
NDImage
|
input immunohistochemistry image. |
required |
dab_thr |
float
|
minimum value to use for thresholding. |
0.03
|
object_min_size |
int
|
the smallest allowable object size. |
1000
|
hole_min_size |
int
|
the smallest allowable hole size. |
1000
|
tissue_mask |
Optional[NDBoolMask]
|
mask to use on input image. |
None
|
he |
Optional[NDImage]
|
input H&E image. If specified, pixels where DAB value is high for both |
None
|
binary_op |
Optional[Callable]
|
must be a binary operation from |
None
|
r |
int
|
radius of the disk to use as footprint for |
10
|
Returns:
| Type | Description |
|---|---|
NDBoolMask
|
DAB thresholded mask. |
get_mask_AE1AE3(he, ihc)
Compute mask on paired AE1AE3 immunohistochemistry and H&E images.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
he |
Union[Image, NDImage]
|
input H&E image. Mask is computed using a threshold on H channel. |
required |
ihc |
Union[Image, NDImage]
|
input immunohistochemistry image. Mask is computed using a threshold on DAB channel. |
required |
Returns:
| Type | Description |
|---|---|
NDBoolMask
|
Intersection of H&E and IHC masks. |
get_mask_PHH3(he, ihc)
Compute mask on paired PHH3 immunohistochemistry and H&E images.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
he |
Union[Image, NDImage]
|
input H&E image. Mask is computed using a threshold on H channel. |
required |
ihc |
Union[Image, NDImage]
|
input immunohistochemistry image. Mask is computed using a threshold on DAB channel. |
required |
Returns:
| Type | Description |
|---|---|
NDBoolMask
|
Intersection of H&E and IHC masks. |
get_mask_function(ihc_type)
Get mask function corresponding to an immunohistochemistry type.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ihc_type |
str
|
name of the IHC technique. |
required |
Returns:
| Type | Description |
|---|---|
Callable
|
Corresponding masking function. |
get_tissue_mask(img_G, blacktol=0, whitetol=247)
Get basic tissue mask from grayscale image.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
img_G |
NDByteGrayImage
|
grayscale input image as numpy byte array. |
required |
blacktol |
int
|
minimum value to be considered foreground. |
0
|
whitetol |
int
|
maximul value to be considered foreground. |
247
|
Returns:
| Type | Description |
|---|---|
Mask as a boolean array. |
update_full_mask(full_mask, mask, x, y)
Update a portion of a large mask using a smaller mask.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
full_mask |
NDBoolMask
|
large mask to update. |
required |
mask |
NDBoolMask
|
small mask to use for update. |
required |
x |
int
|
x coordinate of top-left corner of |
required |
y |
int
|
y coordinate of top-left corner of |
required |
update_full_mask_mp(full_mask, mask, x, y, w, h)
Update a portion of a large mask using a smaller mask.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
full_mask |
Array
|
large mask to update. |
required |
mask |
NDBoolMask
|
small mask to use for update. |
required |
x |
int
|
x coordinate of top-left corner of |
required |
y |
int
|
y coordinate of top-left corner of |
required |