Commit 0a8feffc authored by Christoph Sommer's avatar Christoph Sommer

added demo data link, added Fiji tipps

parent 4b5dac2c
......@@ -15,6 +15,17 @@ The training of a neural network is done iteratively in `epochs`. In each epoch,
4. Select training parameters and execute training code block.
#### Seting up Fiji for prediction with CARE models
Using Tensorflow 1.12.0 / NVidia toolkit 9.0
1. Use the Fiji [CSBDeep](http://sites.imagej.net/CSBDeep/) update site
Using Tensorflow 1.13.1 / NVidia toolkit 10.0
1. get libtensorflow-1.13.1.jar and [tensorflow_jni.dll](https://www.tensorflow.org/install/lang_java)
2. put libtensorflow_jni-1.13.1.jar into "Fiji.app\jar\"
3. put tensorflow_jni.dll into folder "Fiji.app\lib\win64\"
Restart Fiji
#### Using the trained network for prediction
You can predict new images in the IPython notebook directly using the prediction widgets, or use the Fiji:
......@@ -66,6 +77,13 @@ jupyter nbextension enable --py widgetsnbextension
```
More information on [Jupyter/IPython widgets](https://ipywidgets.readthedocs.io/en/stable/user_install.html).
### Example data
The authors of [CARE](https://github.com/CSBDeep/CSBDeep/tree/master/examples) provide example data from different modalities.
* [3D denoising](http://csbdeep.bioimagecomputing.com/example_data/tribolium.zip)
Unzip, copy and rename (e. g. *_low.tif*, *_high.tif*) the images form `low` and `GT` into a single folder.
### Troubleshooting and known issues
* tensorflow 1.13.x requires NVidia tookit 10.0 for the latest csbdeep 0.3.0 release.
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