hip-satomi / microbeseg Goto Github PK
View Code? Open in Web Editor NEWDeep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data
License: MIT License
Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data
License: MIT License
Enables inference on servers without the need for a connection with graphical user interface.
Required:
Window logo not loaded in message boxes.
Only for the owner "true" is returned.
Enables training on servers without the need for a connection with a graphical user interface.
So far, microbeSEG extracts the selected channel from the images. However, there may be cases, where the rgb information should be kept for annotation and model training, e.g. for histopathological images.
Goal: branch with rgb support (data cropping, model training + augmentation, inference)
Path.cwd() is not a good choice since it may return another directory than the microbeSEG directory.
Upload on zenodo models trained on hip-satomi, omnipose and cell tracking challenge data.
Adjust readme to cite also omnipose and cell tracking challenge when model trained on omnipose is used.
When copying images in OMERO, e.g., into another dataset/project, the copied image is just a link to the original image. In that case, 'getProject' returns a NoneType Object without attribute 'getName'. Use 'listParents' to see if an image has been copied and is linked to multiple datasets/projects.
For some data upsampling may be usefull for annotation and segmentation, e.g., object width smaller than 3-4 px. In addition, some data just differ in resolution and down- or upsampling may enable to use another available already trained model without the need for new annotations.
Some menus do not adapt well when maximizing them.
no window maximization icon on windows but a useless "?" icon
Could be benefitial to retrain one of the published models instead of training from scratch. This needs some deep evaluation (learning rates of the first deep layers vs output layers, layer freezing, ...).
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