Cellularity estimation
ADC_to_cellularity(ADC, roi_enhance, roi_nonenhance=None)
Converts an ADC map to a cellularity map using region of interest (ROI) masks.
This function calculates the cellularity for enhancing and non-enhancing regions based on the apparent diffusion coefficient (ADC) values. Cellularity for non-enhancing regions is set to a fixed literature-based constant.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ADC
|
Image3D
|
The measured apparent diffusion coefficient (ADC) map. |
required |
roi_enhance
|
Image3D
|
Binary mask for enhancing regions (e.g., tumors). |
required |
roi_nonenhance
|
Image3D
|
Binary mask for non-enhancing regions. |
None
|
Returns:
| Name | Type | Description |
|---|---|---|
Image3D |
T
|
The computed cellularity map, normalized between 0 and 1. |
Raises:
| Type | Description |
|---|---|
AssertionError
|
If input images have mismatched shape or spacing. |
compute_carrying_capacity(brain_mask, cell_size_mm=1e-06, packing_fraction=0.75)
Computes the physical carrying capacity (maximum number of cells) for a voxel.
The carrying capacity is calculated based on the voxel volume, a packing fraction, and the average size of a cell.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
brain_mask
|
Image3D
|
Binary mask of the brain region. |
required |
cell_size_mm
|
float
|
Average cell size in mm³. Default is 1e-6 mm³. |
1e-06
|
packing_fraction
|
float
|
Fraction of voxel space occupied by cells. Default is 0.75. |
0.75
|
Returns:
| Name | Type | Description |
|---|---|---|
float |
float
|
The carrying capacity for a single voxel (cells per voxel). |
Raises:
| Type | Description |
|---|---|
ValueError
|
If the unit of the brain mask spacing is invalid. |