BiaPy
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BiaPyX
Open source Python library for building bioimage analysis pipelines
Hello, I used the Biapy GUI to train an UNET (Semantic Segmentation template) on 2D with RGB images (slide scanner image). I would like to predict a large image (1.5GB)....
Hi @danifranco I've trained a model using percentile normalization with the 3D detection workflow. I'm running into errors during the "TEST" part of the workflow. I keep getting this error:...
Hello Dani! Please can you extend the support for loading and patching from multiple datasets (such as labels and raw) stored within `one` zarr. The zarr organisation may look like:...
The idea is to have more options apart from ``DATA.TRAIN.MINIMUM_FOREGROUND_PER``. Intensity based measurements seem to be useful for users, e.g. mean, min/max, std (see [forum.sc thread](https://forum.image.sc/t/neuron-cell-detection-biapy/94198/10)).
[imgaug ](https://github.com/aleju/imgaug) project is not being updated. We should implement the transformations used through imgaug to remove its dependecy completely. The transformations are these: - [x] #63 - [x] Random...
Add the option to retrain BMZ models, not just to do inference. There are two options we can do: - Use Torchscript directly loaded models and work with that (possible...
We need to implement `after_merge_patches_by_chunks_proccess_patch` function ([here](https://github.com/danifranco/BiaPy/blob/97603fbf4b94a22112c6504105fd13cb06d9a954/engine/instance_seg.py#L373)). Instance creation needs to be done by patches and then merge. Example in [cellpose code](https://github.com/MouseLand/cellpose/blob/main/cellpose/contrib/distributed_segmentation.py).
Add support for reading `.nii.gz` data. Something was done in [load_ct_data_from_dir](https://github.com/danifranco/BiaPy/blob/befef89d03043489b80dc3b2f4da7d0645248836/utils/util.py#L980) function. Need to incorporate it to `load_data_from_dir` and `load_3d_images_from_dir` function for reading 2D and 3D images respectively. We can...
So far, only PSNR is implemented. Possible metrics to include are: - SSIM - MAE - MSE - Perceptual metrics - ... @IvanHCenalmor
I have included the necessary blocks to create the second version of the U-NeXt model (U-NeXt-V2): - In **blocks.py:** I added a GRN (Global Response Normalization) block, as well as...
