Commit 130e2347 authored by Constantin Pape's avatar Constantin Pape

Update README.md

parent cee36a34
......@@ -41,12 +41,18 @@ CUDA_VISIBLE_DEVICES=0 train_stardist_2d /path/to/data /path/to/model
CUDA_VISIBLE_DEVICES=0 predict_stardist_2d /path/to/data /path/to/model
```
Here, `/path/to/data` is where the data for training / prediction is stored.
It should be stored [in this data layout](https://git.embl.de/grp-bio-it/ai4ia#data-layout).
Note that you don't need the `labels` folder for the prediction script.
`/path/to/model` specifies where the model should be saved in the training script and where to load it from in the prediction script.
The `CUDA_VISIBLE_DEVICES=0` part determines which gpu is used. If you have a machine with multiple GPUs and don't want to
use the first one, you need to change the `0` to the id of the GPU you want to use.
In order to run these scripts on the embl via slurm, you can use the `submit_slurm` script from `deep_cell.utils`, e.g.
In order to run these scripts on the embl via slurm, you can use the `submit_slurm` script from `ai4ia.utils`, e.g.
```
submit_slurm train_stardist_2d /path/to/data /path/to/model
```
Scripts to train and predict with a 3d stardist model are also available: `train_stardist_3d`, `predict_stardist_3d`.
Scripts to train and predict with a 3d stardist model are also available: `train_stardist_3d`, `predict_stardist_3d`. They and can be used in the same way as the scripts for 2d.
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