in part 3 of the Neubias talk on StarDist it was mentioned that for training of an appropriate classifier the EPFL adds the 15 annotated ROIs of the respective project to the dataset of the data-science-bowl-2018-train images (https://bbbc.broadinstitute.org/BBBC038). Now I have annotated my pictures and wanted to proceed just like that, when I came to realise that the BBC dataset has a different structure with masks and images in subfolders which are named after the image file, and with the multiple masks not having a corresponding nomenclature. How do you solve this difference? I have tried to upload it to the Jupyter notebook and also to merge them into one images and one masks folder, but it gives me an assertion error due to the different file-names: So does anyone have an adjusted dataset (which he/she could share?) or an adjusted code of the notebook?
I have linked a picture of the different folder structures and am happy to give you further information.
Thanks so much!!!