Constants¶
Fixed quantities used by the released ALHENA model, including image geometry, retrieval defaults, annotation axes, and the tissue-reference registry.
The built-in annotation axes are distinct
lineage_v1 and compartment_v1 define different classification tasks. Interpret annotations
and evaluation metrics separately for each axis.
Not importable from the package
Thirteen names here live in alhena._constants alone: TOKEN_GRID, NUM_TOKENS,
UNKNOWN_LABEL, MPP_TOLERANCE, CROP_WARNING_FRACTION, MIN_MICROSCOPE_MPP,
MAX_MICROSCOPE_MPP, MIN_REFERENCE_CELLS_PER_CLASS, MIN_SUPPORT_TO_K_RATIO,
MIN_K_TO_CLASSES_RATIO, BACKBONE_REPO, WEIGHTS_REPO and REFERENCES_REPO. The remaining
constants are re-exported from the top-level package, so alhena.REFERENCE_MPP, for example,
refers to the same value.
module-attribute
¶
Microns per pixel the encoder reads, which tiles of a declared resolution are brought to.
module-attribute
¶
Native microns per pixel of UNI2-h, an operating point nothing resamples to.
module-attribute
¶
Side of the square canvas the encoder reads, in pixels.
module-attribute
¶
Side of one token, in pixels of the canvas.
module-attribute
¶
Reference neighbors each cell votes over.
module-attribute
¶
Softmax temperature over neighbor similarities.
module-attribute
¶
Neighbors retrieved, then scored again pair by pair, before the slice to k.
module-attribute
¶
Classes of the lineage_v1 axis, in the order of their codes (label_order).
module-attribute
¶
Classes of the compartment_v1 axis, in the order of their codes (label_order).
module-attribute
¶
CLASS_AXES = {'lineage_v1': LINEAGE_V1, 'compartment_v1': COMPARTMENT_V1}
Declared class axes, by name.
module-attribute
¶
Class axis used where none is named.
Return the class order of an axis, scorable classes sorted, then the unknown class.
The order fixes the code of every class and breaks ties in the vote.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
axis
|
str
|
A key of |
required |
Returns:
| Type | Description |
|---|---|
tuple[str, ...]
|
Class names in their canonical order. |
Raises:
| Type | Description |
|---|---|
AlhenaValueError
|
If the axis is not one of the declared axes. |
module-attribute
¶
CLASS_COLORS = {'T_NK': (255, 15, 15), 'B_Plasma': (255, 143, 15), 'Myeloid': (255, 211, 15), 'Immune': (255, 123, 15), 'Stromal_Vascular': (113, 191, 18), 'Epithelial_Melanocyte': (39, 188, 178), 'Unknown': (143, 143, 143)}
RGB color of each class in the figures of alhena.viz.
module-attribute
¶
TISSUE_TO_SHARD = {'Breast': 'breast', 'BoneMarrow': 'bone_marrow', 'Cervix': 'cervix', 'Colon': 'intestine', 'Heart': 'heart', 'Kidney': 'kidney', 'Liver': 'liver_cell', 'Lung': 'lung', 'LymphNode': 'tonsil', 'Ovary': 'ovary', 'Pancreas': 'pancreas_cell', 'Prostate': 'prostate', 'Skin': 'skin', 'Tonsil': 'tonsil', 'Uterus': 'uterus'}
Shard each tissue is served by, under its canonical organ name; tissues may share one.
module-attribute
¶
TISSUE_ALIASES = {'Colonic': 'Colon', 'Cutaneous': 'Skin', 'Hepatic': 'Liver', 'Mammary': 'Breast', 'Ovarian': 'Ovary', 'Pancreatic': 'Pancreas', 'Prostatic': 'Prostate', 'Pulmonary': 'Lung', 'Renal': 'Kidney', 'Tonsillar': 'Tonsil', 'Uterine': 'Uterus', 'Cervix uteri': 'Cervix', 'Prostate gland': 'Prostate', 'Uterine cervix': 'Cervix', 'Bowel': 'Colon', 'Colorectal': 'Colon', 'Large intestine': 'Colon', 'Rectum': 'Colon', 'Small intestine': 'Colon', 'Corpus uteri': 'Uterus', 'Endometrium': 'Uterus', 'Myometrium': 'Uterus'}
Other names a tissue is accepted under, each mapped to its tissue in TISSUE_TO_SHARD.
module-attribute
¶
TOKEN_GRID = INPUT_SIZE // PATCH_SIZE
Tokens along each side of the canvas.
module-attribute
¶
NUM_TOKENS = TOKEN_GRID * TOKEN_GRID
Patch tokens of one canvas.
module-attribute
¶
Name of the unknown class, last in every class order, which no row is coded with.
module-attribute
¶
Relative difference between a declared mpp and the target above which tiles are resampled.
module-attribute
¶
Share of a field the center crop may discard before a GeometryWarning is raised.
module-attribute
¶
Finest microns per pixel of a microscope image: a tenth of the 0.2 micron a lens resolves.
module-attribute
¶
Coarsest microns per pixel of a microscope image, between a 1.25x scan and 600 dpi.
module-attribute
¶
Reference cells below which a class is reported as thinly supported.
module-attribute
¶
Floor of the thinnest class's support over k, below which EnvelopeWarning is raised.
module-attribute
¶
Floor of k over the number of classes, below which EnvelopeWarning is raised.
module-attribute
¶
Model hub repository of the UNI2-h weights, gated by their authors.
module-attribute
¶
Model hub repository publishing the encoder bundle.
module-attribute
¶
Model hub repository publishing the reference shards and their registry.
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