EmbedSeg
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juglab
Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images
**Describe the bug** I am trying the example notebooks and successfully ran 01-data However, when I try the training notebook and being training the model, it takes a long time...
Hello. I tried tutorial of bbbc010-2012 Jupyter notebooks, but this error happend and I don't know solution. Could you tell me what I should do ? I ran 01-data.ipynb and...
I have 4 images, and batch size is only 1. but when I start the `begin_training(train_dataset_dict, val_dataset_dict, model_dict, loss_dict, configs)`, I have RuntimeError: CUDA out of memory. Tried to allocate...
Hi there! I'm updating the [Embedseg notebook in ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/EmbedSeg_2D_ZeroCostDL4Mic.ipynb) so we can also use it in [DL4MicEverywhere](https://github.com/HenriquesLab/DL4MicEverywhere) with Docker containers. For the containerisation in Mac we are having some issues...
**Describe the bug** In the [bbbc010-2012 predict notebook](https://github.com/juglab/EmbedSeg/blob/main/examples/2d/bbbc010-2012/03-predict.ipynb), the default cell loading the pre-trained model fails. It seems it cannot load the `state_dict` because the module path has changed (`encoder.initial_block.conv.weight`...
I am trying to train the model with 02-train.ipynb on the available CTC data since the pretrained model is not available online. I get the following error: RuntimeError Traceback (most...
Hello team, I am trying to run the 3 DSB notebooks from the examples on my macbook (no GPU), and I run into the error `FileNotFoundError: [Errno 2] No such...
**Describe the bug** I cannot find the json file mentioned in file EmbedSeg/tree/main/examples/2d/dsb-2018/03-predict.ipynb. This file is important for configuring evaluation process. The code from notebook is as follows. `torch.hub.download_url_to_file(url =...
Hello, I found your links of pretrained models in this [project page](https://github.com/juglab/EmbedSeg) are 404. Do they still available? I want to try your models on our private dataset of 3D...
