Manan Lalit

I speak only as a reader of the publication, the authors would be able to give a more informed answer: 1. It should be possible to track on custom datasets....

Hello @kenta-takizawa, Thanks for looking into `EmbedSeg`! Could you also please share the `01-data` and `02-train` notebooks which you ran as well (for example, by exporting them to html. This...

Hello @Saharkakavand. Thank you for opening an issue and trying out _EmbedSeg_! Could you share the size of the original images and the `crop_size` which you used in `01-data.ipynb`? A...

Okay, so these look like confocal volume images since the size of the _z_ dimension appears almost the same as _x_ and _y_ dimensions, is that correct? [This](https://github.com/juglab/EmbedSeg/blob/main/examples/3d/Platynereis-ISH-Nuclei-CBG/01-data.ipynb) set of...

Hello @Saharkakavand Thanks for giving this a go. To me, the loss after 60 epochs looks reasonable- probably a better indicator of whether the training is stagnating is by looking...

The `iou` profile appears strange to me- my understanding is that the iou shouldn't really go down unless the validation and train images are quite different in their appearance. Would...

I am guessing this is similar to the related [issue](https://github.com/danielfrg/mkdocs-jupyter/issues/170#issue-1910109868) but not the same maybe, since the cell is not executed as opposed to the output being hidden?

Hello @codingS3b Thank you for looking into this and also for your pull request (I will get to it hopefully next week!). On this question front, I wanted to ask...

Hello @lphilomena So the `01-data.ipynb` [notebook](https://github.com/juglab/EmbedSeg/blob/main/examples/2d/bbbc010-2012/01-data.ipynb) downloads data from this url `https://github.com/juglab/EmbedSeg/releases/download/v0.1.0/bbbc010-2012.zip`. If you manually download from this url and unzip this folder, you would see a directory called `train/masks`...

Hi @lphilomena These 100 masks are all multi-slice tiffs, with the number of slices in each mask equal to the number of worms present in the corresponding image. In each...