pathology/nuclick/nuclick_infer.ipynb #1542
Comments
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The data doesn't appear to be accessible to the public. Can we skip the tutorials on this data and just add some comments in the tutorial? |
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sure, please help skip the tests for now, and if the datasets are permanently removed, we'll need to redesign the tutorials. |
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I just noticed this issue Project-MONAI/MONAI#5412. cc @drbeh |
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I checked their website and it seems that this dataset is temporarily not available! I will check with the Warwick university to see what's going on. |
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Thanks for the confirmation. Sure, I will skip the test for now. If there is no problem with the license, we may be able to put it in extra data. I remember that the zip size is only 154 MB. |
Signed-off-by: KumoLiu <yunl@nvidia.com>
Fixes #1542. ### Description Temporarily skip the tutorials related to the CoNSep dataset. After confirming with the Warwick University, [Tissue Image Analytics (TIA) Centre](https://warwick.ac.uk/fac/cross_fac/tia/), may remove the dataset to extra data repo or google drive. ### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Avoid including large-size files in the PR. - [ ] Clean up long text outputs from code cells in the notebook. - [ ] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>` Signed-off-by: KumoLiu <yunl@nvidia.com>
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Just skip the tests for now at #1544. |
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Hi @drbeh, have you had a chance to get in touch with Warwick University and can we move the data? |
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Hi @KumoLiu, I have talked to them a while ago about the CoNSeP dataset but it was not clear what was the plan for this dataset. @shaneahmed do you have any update here? Is this dataset going to be available on TIA homepage, or should we make a mirror for this? |
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#1542. ### Description Temporarily skip the tutorials related to the CoNSep dataset. After confirming with the Warwick University, [Tissue Image Analytics (TIA) Centre](https://warwick.ac.uk/fac/cross_fac/tia/), may remove the dataset to extra data repo or google drive. ### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Avoid including large-size files in the PR. - [ ] Clean up long text outputs from code cells in the notebook. - [ ] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>` Signed-off-by: KumoLiu <yunl@nvidia.com>
https://warwick.ac.uk/fac/cross_fac/tia/data/hovernet/consep_dataset.zip not available
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