I would like to use a photo, then use the fill tool and a low threshold, so that it fills only the contours. But after the feeling I want to delete the photo and only keep the fillings. How could I do that? Because if I have a new layer, it doesn't work with the filing, as there are not contours, and if I use it directly on the photo, I can't delete it. Is there a way?

All depends on the image and usually each image has to be considered on its own. If looking for a batch process, unlikely.

Bucket fill with similar colours and threshold?? A colour selection with threshold and in additive mode to build up a selection might be better. Invert selection, cut out background.

Always a better way because it is non-destructive, is a layer-mask. This example:

[img]https://i.imgur.com/pLBJE2h.jpg[/img]

1. Trying to isolate the cell borders: Very common with gimp to duplicate layers and work on the duplicate.

2. This using Colours -> Threshold to produce a binary image Black for transparent, White for solid. There are other ways, depends on the image Gimp has a whole set of edge detect filters.

[img]https://i.imgur.com/AupqAPo.jpg[/img]

3. The original image has a (white) layer mask added: Layer -> Mask -> Add layer mask. The black/white layer is copied and pasted into the layer mask.

4. With a solid background.

That is a basic image. The layer-mask can be edited same as any other layer. Paint in black to hide / white to uncover or other tools to improve the result.