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https://github.com/mmasoud1/dsa_reg
https://github.com/mmasoud1/dsa_reg
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/mmasoud1/dsa_reg
- Owner: Mmasoud1
- Created: 2020-07-14T14:33:36.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-07-16T15:00:49.000Z (over 4 years ago)
- Last Synced: 2024-11-14T23:44:13.013Z (about 2 months ago)
- Language: Python
- Size: 10.7 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## dsa_reg
This package approximately computes the offsets needed to register DSA (Digital Slide Archive) item thumbnails.
## Installations
__Through pypi package__
``` Shell
$ pip install dsa-reg
```
__From Source__
``` Shell
$ git clone [email protected]:mmasoud1/dsa_reg.git
```
## Usage
After the package is installed, main operation can be performed as follows:
__Register by Thumbnails__
``` Python
from dsa_reg import rigidRegByThumb
#param refItemId (string): ref image Id
#param targetItemId (string): target image Id
#param xBaseUrl (string): DSA Server URL e.g. https://styx.neurology.emory.edu/girder/api/v1
#param xAuthentication: boolean (0,1)
#param xEnhancement: boolean (0,1)
#return (Dict): homography metrix, psnr, x offset, y offset, horizontal scaleX, vertical scaleY
rigidRegByThumb(refItemId, targetItemId, xBaseUrl)
# e.g.
rigidRegByThumb(refItemId = "5e361da534679044bda81b16",
targetItemId = "5e361-SOME-OTHER-ID",
xBaseUrl = "https://styx.neurology.emory.edu/girder/api/v1")
# if using a private DSA collection, set xAuthentication = 1 to provide login credentials:
rigidRegByThumb(refItemId = "5e361da534679044bda81b16",
targetItemId = "5e361-SOME-OTHER-ID",
xBaseUrl = "https://styx.neurology.emory.edu/girder/api/v1",
xAuthentication = 1,
xEnhancement = 0)
# If a preprocessing is needed such that the tile needs enhancement before registration, set xEnhancement boolean value to 1
```
__Register by Magnification__
``` Python
from dsa_reg import rigidRegByMagnification
rigidRegByMagnification(refItemId, targetItemId, xBaseUrl)
#e.g.
rigidRegByMagnification(refItemId = "5e361da534679044bda81b16",
targetItemId = "5e361-SOME-OTHER-ID",
xBaseUrl = "https://styx.neurology.emory.edu/girder/api/v1")
# magnification default value is 1
rigidRegByMagnification(refItemId, targetItemId, xBaseUrl, magnification, xAuthentication)
# magnification can be smaller value < = 1 for fast processing and wise resources use
rigidRegByMagnification(refItemId, targetItemId, xBaseUrl, magnification, xAuthentication, xEnhancement)
#e.g.
rigidRegByMagnification(refItemId = "5e361da534679044bda81b16",
targetItemId = "5e361-SOME-OTHER-ID",
xBaseUrl = "https://styx.neurology.emory.edu/girder/api/v1",
magnification = 0.5,
xAuthentication = 1,
xEnhancement = 1)
```
## For contributing, issues and suggestions
Your contribution to enhance the registration technique is welcomed, please start by new issue or pull a request.
### Next:
1. This is a demo of initial and approximated rigid registration results, the target is to extend the functionality to whole slide images registration in fast, accurate mode.