Datasets¶
We include multiple dataset loading utilities. Note that for some functions
implemented in the atlalign.data
module we assume that the user has
the underlying raw data locally.
Nissl volume¶
Contains the 25 microns reference volume used within the entire project. The corresponding function
is nissl_volume
that returns a (528, 320, 456, 1) numpy array.
Annotation volume¶
Contains per pixel segmentation/annotation of the entire reference atlas. The corresponding
function is annotation_volume
that returns a (528, 320, 456) numpy array. Note
that one can use the corresponding segmentation_collapsing_labels
function
to get the tree-like hierarchy of the classes.
Manual registration¶
This dataset comes from the labeling tool that extracts displacement fields. The corresponding function is
manual_registration
.
Available genes:
Calb1
Calb2
Cck
Npy
Pvalb
Sst
Vip
from atlalign.data import manual_registration
res = manual_registration()
assert set(res.keys()) == {'dataset_id', 'deltas_xy', 'image_id', 'img', 'inv_deltas_xy', 'p'}
assert len(res['image_id']) == 278
The returned dictionary contains the following keys:
dataset_id
- unique id of the section dataset
deltas_xy
- array of shape (320, 456, 2) where the last dimension represents the x (resp y) deltas of the transformation
image_id
- unique id of the section image
img
- moving image of shape (320, 456) that was preregistered with the Allen API
inv_deltas_xy
- same asdeltas_xy
but represents the inverse transformation
p
- coronal coordinate in microns [0, 13200]
To perform the registration instantiate atlalign.base.DisplacementField
using the deltas_xy
and warp the
img
with it.
from atlalign.base import DisplacementField
from atlalign.data import manual_registration
import numpy as np
res = manual_registration()
i = 10
delta_x = res['deltas_xy'][i, ..., 0]
delta_y = res['deltas_xy'][i, ..., 1]
img_mov = res['img'][i]
df = DisplacementField(delta_x, delta_y)
img_reg = df.warp(img_mov)
For more details on atlalign.base.DisplacementField
see Building Blocks.
Dummy¶
Artificially generated datasets.
Rectangles¶
Rectangles with stripes of different intensities. Corresponding function - rectangles
.
Circles¶
Circles with inner circles of different intensities. Corresponding function - circles
.