Comments (2)
Hi @mariamhrr , at the moment we don't have any concrete example of 2d image segmentation and png format is not supported. Contributions are welcomed!
from niftynet.
@mariamhrr @wyli Since the merge of image-loader NiftyNet now fully supports 2D images without having to convert them to NiftyFormat. There is no need to fake 3-dimensional spatial_window_size
either (although it is perfectly ok if you do).
NiftyNet currently supports loading images from OpenCV, Scikit-Image and PIL/Pillow, assuming that you have the corresponding libraries installed. You can specify a loader in the config file, or it will automatically try to find one that can handle yout images.
Pretty much every 2D image format is supported (as long as it can be loaded by one of those libraries): .jpg, .png, .bpm, .tif ...
For more information check image_loader.py.
Example configuration file:
[images]
path_to_search = ~/data/test_image_segmentation/
filename_contains = bmp
spatial_window_size = (224, 224)
interp_order = 1
loader = opencv
[masks]
path_to_search = ~/data/test_image_segmentation/
filename_contains = _mask
spatial_window_size = (224, 224)
interp_order = 0
loader = skimage
from niftynet.
Related Issues (20)
- Expected size of adding custom dataset for classification task on MR dataset?
- Provided indices are out-of-bounds w.r.t. dense side with broadcasted shape. Histogram error? HOT 1
- Using GANs without conditioning
- upgrade to support tensorflow 1.15
- If Niftynet supports Xavier initialization?
- Remove unconnected islands
- Default values for the bias field layer might be too large
- Float comparison in histogram normalisation layer
- Handle SimpleITK's lack of thread safety
- Sections containing `csv_data_file` are not loaded
- AdamW optimizer
- TensorRT frozen graphs - integration with NiftyNet
- Feature: Rewrite NiftyNet to use TensorFlow 2.0 HOT 1
- Using NiftyNet to do segmentation of MRI scans(in .nii extension) to grey matter,white matter and csf
- NiftiNet Roadmap HOT 2
- Niftynet window aggregator function for inferens - explaination needed
- using other DL framework
- How to train a model with one input and multi-output?
- dense-vnet to Monai HOT 1
- Segmentation classes description not available
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from niftynet.