Deepflash2

New Features

- Instance segmentation metrics ([32](https://github.com/matjesg/deepflash2/pull/32)), thanks to [matjesg](https://github.com/matjesg)
- - Instance segmentation metrics for GT estimation and prediction
- Tutorials

New Features

- Adding tifffile imread ([13](https://github.com/matjesg/deepflash2/pull/13)), thanks to [matjesg](https://github.com/matjesg)
- Closes 12

- Multichannel tiffs are imported as single channel greyscale when imported via ui ([12](https://github.com/matjesg/deepflash2/issues/12))
- Problem: .tiff images are with shape z,c,y,x = 1,4,1024,2048 are selected in the user deepflash google colab user interface. Image preview only shows first channel. After inspecting the image import, I saw, that the tiffile has dimensions 1024x2048 after import.

Proposed solution: Images may be imported with tifffile.imread instead of imageio.imread. Here, the channel dimensions are preserved.

New Features

- Real-Time loss weight computation and large file support ([11](https://github.com/matjesg/deepflash2/pull/11)), thanks to [matjesg](https://github.com/matjesg)
- - Real-Time loss weight computation via fast convolutional distance transform on GPU
- temp storage using zarr instead of RAM
- zarr dependency

Bugs Squashed

- Prediction not possible on Windows machines due to cuda error ([10](https://github.com/matjesg/deepflash2/issues/10))
- During prediction on a windows machine a a OS Error occurs due to:

"RuntimeError: cuda runtime error (801) : operation not supported at ..\torch/csrc/generic/StorageSharing.cpp:247"

Problem: Storage sharing currently not supported on windows.

Proposed solution: Ensemble learner takes "num_workers" argument and passes it to subsequent functions. If num_workers == 0, prediction works for me.

- Bug fixes and minor improvements.

New Features

- Adding GUI and new project structure ([8](https://github.com/matjesg/deepflash2/pull/8)), thanks to [matjesg](https://github.com/matjesg)

New Features

- Adding test time augmentation ([7](https://github.com/matjesg/deepflash2/pull/7)), thanks to [matjesg](https://github.com/matjesg)

Bugs Squashed

- Type Error when starting training ([5](https://github.com/matjesg/deepflash2/issues/5))
- When I try to start the training process in google colab, this error occurs:

**TypeError: no implementation found for 'torch.nn.functional.cross_entropy' on types that implement __torch_function__: [<class 'fastai.torch_core.TensorImage'>, <class 'fastai.torch_core.TensorMask'>]**

as well as

**FileNotFoundError: [Errno 2] No such file or directory: 'models/model.pth'**

in the end.


Hope you know whats the problem.