Robust quad-tree based registration on whole slide images
Project description
Robust quad-tree based registration on whole slide images
This is a library that implements a quad-tree based registration on whole slide images.
Core features
- Whole Slide Image support
- Robust and fast
- Rigid and non-rigid transformation
Additional Requirements
Notebooks
Example notebooks are in the demo folder or .
Ho-To:
Import package and create Quad-Tree.
import qt_wsi_reg.registration_tree as registration
parameters = {
# feature extractor parameters
"point_extractor": "sift", #orb , sift
"maxFeatures": 512,
"crossCheck": False,
"flann": False,
"ratio": 0.6,
"use_gray": False,
# QTree parameter
"homography": True,
"filter_outliner": False,
"debug": False,
"target_depth": 1,
"run_async": True,
"num_workers: 2,
"thumbnail_size": (1024, 1024)
}
qtree = registration.RegistrationQuadTree(source_slide_path=Path("examples/4Scanner/Aperio/Cyto/A_BB_563476_1.svs"), target_slide_path="examples/4Scanner/Aperio/Cyto/A_BB_563476_1.svs", **parameters)
Show some registration debug information.
qtree.draw_feature_points(num_sub_pic=5, figsize=(10, 10))
Show annotations on the source and target image in the format:
[["center_x", "center_y", "anno_width", "anno_height"]]
annos = np.array([["center_x", "center_y", "anno_width", "anno_height"]])
qtree.draw_annotations(annos, num_sub_pic=5, figsize=(10, 10))
Transform coordinates
box = [source_anno.center_x, source_anno.center_y, source_anno.anno_width, source_anno.anno_height]
trans_box = qtree.transform_boxes(np.array([box]))[0]
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
qt-wsi-registration-0.0.12.tar.gz
(18.3 kB
view hashes)
Built Distribution
Close
Hashes for qt-wsi-registration-0.0.12.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 30df8ea5034167fcd2a235bbc61977528e12370be64ecbeb43866545a1c00afb |
|
MD5 | 9848a3ccd4f35b570aa361c516c4595c |
|
BLAKE2b-256 | f48ec475f7127bd7354d4fb5b699c5b269b19ae76f666a7de9d634cb2e574db7 |
Close
Hashes for qt_wsi_registration-0.0.12-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f365e287905e839d3d74407b1289eabf803c05d029760baa4de1292e88473fc8 |
|
MD5 | 0895b64c3a647772fd36d2793371b7b4 |
|
BLAKE2b-256 | c551ef76faa62aa2a6ae00fd2a4daa0689e137ed94d8dd872a4a7cad7348f195 |