Recent Releases of deepflash2
deepflash2 - v0.2.1
-- Bug fixes -- Adding Code-based Tutorial (https://matjesg.github.io/deepflash2/tutorial_monuseg.html)
- Jupyter Notebook
Published by matjesg over 3 years ago
deepflash2 - v0.2.0
New Features
new features (#42), thanks to @matjesg
- Multiclass GT Estimation, closes #34
- Torchscript ensemble class for inference / tta adjusted
- ONNX export possible
Major changes
- Different classes for training (EnsembleLearner) and Inference (EnsemblePredictor)
- Normalization based on uin8 images (0...255)
Instance segmentation metrics (#32), thanks to @matjesg
- Instance segmentation metrics for GT estimation and prediction
- Jupyter Notebook
Published by matjesg over 3 years ago
deepflash2 - Trained models for deepflash2 paper
- Jupyter Notebook
Published by matjesg over 3 years ago
deepflash2 - v0.1.8
- Dependency fix (opencv-python-headless>=4.1.1,<4.5.5)
- Minor improvements and fixes
- Jupyter Notebook
Published by matjesg about 4 years ago
deepflash2 - v0.1.7
- Fixes bug when predicting on new data.
- Jupyter Notebook
Published by matjesg about 4 years ago
deepflash2 - Source data for the deepflash2 paper
- Jupyter Notebook
Published by matjesg about 4 years ago
deepflash2 - v0.1.6
- Removing git dependency for cellpose installation.
- Jupyter Notebook
Published by matjesg about 4 years ago
deepflash2 - v0.1.4
New Features
- Instance segmentation metrics (#32), thanks to @matjesg
- - Instance segmentation metrics for GT estimation and prediction
- Tutorials
- Jupyter Notebook
Published by matjesg over 4 years ago
deepflash2 - v0.1.3
New Features
Adding tifffile imread (#13), thanks to @matjesg
- Closes #12
Multichannel tiffs are imported as single channel greyscale when imported via ui (#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.
- Jupyter Notebook
Published by matjesg over 4 years ago
deepflash2 - v0.1.2
New Features
- Real-Time loss weight computation and large file support (#11), thanks to @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)
- 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 "numworkers" argument and passes it to subsequent functions. If numworkers == 0, prediction works for me.
- Jupyter Notebook
Published by matjesg almost 5 years ago
deepflash2 - 0.1.1
0.1.1
- Bud fixes and minor improvements.
- Jupyter Notebook
Published by matjesg about 5 years ago
deepflash2 - 0.0.14
0.0.14
New Features
Bugs Squashed
- Type Error when starting training (#5)
- When I try to start the training process in google colab, this error occurs:
TypeError: no implementation found for 'torch.nn.functional.crossentropy' on types that implement _torchfunction: [<class 'fastai.torchcore.TensorImage'>,
as well as
FileNotFoundError: [Errno 2] No such file or directory: 'models/model.pth'
in the end.
Hope you know whats the problem.
- Jupyter Notebook
Published by matjesg over 5 years ago
deepflash2 - 0.0.13
0.0.13
Bugs Squashed
- Type Error when starting training (#5)
- When I try to start the training process in google colab, this error occurs:
TypeError: no implementation found for 'torch.nn.functional.crossentropy' on types that implement _torchfunction: [<class 'fastai.torchcore.TensorImage'>,
as well as
FileNotFoundError: [Errno 2] No such file or directory: 'models/model.pth'
in the end.
Hope you know whats the problem.
- Jupyter Notebook
Published by matjesg over 5 years ago
deepflash2 - Sample data and models
Sample data and models for demonstration
- Ground truth estimation
- wue1cFOSexpertsegmentationsamples.zip contains 5 segmentation masks from 5 experts each
- Training
- wue1cFOSsmall.zip contains 5 image/mask pairs for training (can also be used for prediction)
- Prediction
- Unetresnet342classes-fold1.pth Trained Model 1
- Unetresnet342classes-fold2.pth Trained Model2
- wue1cFOSsmall.zip contains 5 image/mask pairs
- Jupyter Notebook
Published by matjesg over 5 years ago