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Hi!
First of all congratulations! SPATA2 seems like a very useful tool. In fact, I'm interested in performing a CNV analysis on my 10X Visium data. Here are some questions that I have:
1) What d…
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Thanks for your work! I run the code with our own data for multiple organ segmentation, the results are much worse than those in your paper. May I send our preprocessed data to you to run for a fair …
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I am trying to use AHNet in MONAI instead of Unet for 3D segmentation and cannot figure out the parameters to get the model training.
I'm using nifti CT's with nifti kidney segmentations.
ht…
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Hi, Jun, I want to use DC+HD as the loss to train a multi-organ segmentation model, but I meet two problems:
1. in _nnUNetTrainer_DiceHDBinary.py: from nnunet.training.loss_functions.boundary_loss_…
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Benefit: knowledge of cell count in each spot is very important for simulation for deconvolution, and for analysing data in general. On top of cell segmentations could calculate shape / size statistic…
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Hi, I am trying to do the registration on liver 3d images. I have used antsMultivariateTemplateConstruction2.sh to produce the template using affine and BSplineSyN non-rigid registration. Now, having …
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Could you please generate a matrix of start/end stages, with the following specifications:
- for all anatomical entities in the _composite_ ontology
- with taxon-specific start/end stages for taxon-s…
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Hi, Jun, thank you very much for your valuable work.
When you perform multi-organ segmentation on nnUNet, you observed that the combine of Dice loss and Focal loss achieved the best DSC. Can you sha…
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I am recently worked on the project of cell classification. I hope download the data set of “MULTI-ORGAN NUCLEI SEGMENTATION AND CLASSIFICATION CHALLENGE" for MoNuSAC 2020. I will not share data after…
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Hi, thanks for the repo.
When I try to use the ACELoss, the HD Loss is very high for hundreds epochs (approx. 1e+4) while the DSC is around 0.005 or so. I am wondering if I use this repo right.
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