For the segmentation of single cells I have been using the Cellpose_2D_ZeroCostDL4Mic.ipynb Colab file, which works really nicely with the pre-trained models. However, I would like to train my own model. The program divides the dataset into test and training data in step 4 'Train the network'. Hereafter, when I try to run step 4.2 'Start training' it seems the program does not actually train a model. Below I copied the output when I ran this cell 4.2. Apparently, there are unrecognized arguments, by which I think the training is not initiated. Did someone else encounter this problem and how could I possibly solve it? Thank you in advance.
Hi,
For the segmentation of single cells I have been using the Cellpose_2D_ZeroCostDL4Mic.ipynb Colab file, which works really nicely with the pre-trained models. However, I would like to train my own model. The program divides the dataset into test and training data in step 4 'Train the network'. Hereafter, when I try to run step 4.2 'Start training' it seems the program does not actually train a model. Below I copied the output when I ran this cell 4.2. Apparently, there are unrecognized arguments, by which I think the training is not initiated. Did someone else encounter this problem and how could I possibly solve it? Thank you in advance.
Best, Merijn
usage: main.py [-h] [--version] [--verbose] [--Zstack] [--use_gpu] [--gpu_device GPU_DEVICE] [--check_mkl] [--dir DIR] [--image_path IMAGE_PATH] [--look_one_level_down] [--img_filter IMG_FILTER] [--channel_axis CHANNEL_AXIS] [--z_axis Z_AXIS] [--chan CHAN] [--chan2 CHAN2] [--invert] [--all_channels] [--pretrained_model PRETRAINED_MODEL] [--restore_type RESTORE_TYPE] [--chan2_restore] [--add_model ADD_MODEL] [--no_resample] [--no_interp] [--no_norm] [--do_3D] [--diameter DIAMETER] [--stitch_threshold STITCH_THRESHOLD] [--min_size MIN_SIZE] [--flow_threshold FLOW_THRESHOLD] [--cellprob_threshold CELLPROB_THRESHOLD] [--niter NITER] [--anisotropy ANISOTROPY] [--exclude_on_edges] [--augment] [--save_png] [--save_tif] [--no_npy] [--savedir SAVEDIR] [--dir_above] [--in_folders] [--save_flows] [--save_outlines] [--save_rois] [--save_txt] [--save_mpl] [--train] [--train_size] [--test_dir TEST_DIR] [--mask_filter MASK_FILTER] [--diam_mean DIAM_MEAN] [--learning_rate LEARNING_RATE] [--weight_decay WEIGHT_DECAY] [--n_epochs N_EPOCHS] [--batch_size BATCH_SIZE] [--min_train_masks MIN_TRAIN_MASKS] [--SGD SGD] [--save_every SAVE_EVERY] [--model_name_out MODEL_NAME_OUT] main.py: error: unrecognized arguments: --fast_mode Time elapsed: 0.0 hour(s) 0.0 min(s) 7 sec(s)
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