Inspired from neubias meeting last week I started to play with DeepimageJ. My aim is to deploy models
trained with YAPiC to Fiji. In the long run, I would like to have a function in yapic to export trained models easily to Fiji. Using CSBdeep Fiji Plugin would also be an option. I also tried it, but with DeepImageJ I made more progress so far…
I managed to export a model trained with YAPiC to Tensorflow SavedModel and open it withDeepImageJ. However, there are problems with padding size.
Bundling my model with
DeepImageJ>> DeepImageJ Build Bundled Model works fine:
Input and output size is correctly recognized.
Then I set padding to 214, which is the difference of input and output size:
Next, a test prediction is performed on the test image, this works as expected. The image is tiled and processed:
Until it is finished:
Now, I wand to apply my bundled model by
DeepImageJ>> DeepImageJ Run
However, I get an error, because the padding value is not accepted:
This is strange, because it works without problems in the test run (executed during the Build Bundled Model workflow).
If I set the padding value lower, it is accepted, but tiling does not work correctly any more. Any idea how to solve that?