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me-nobody
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blood_vessel_segment_CNN
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22 Commits
22 Commits
CONDA_environments
CONDA_environments
error_messages
error_messages
1_GBM_WSSM_Prediction.py
1_GBM_WSSM_Prediction.py
GBM_WSSM.py
GBM_WSSM.py
GBM_WSSM_main.py
GBM_WSSM_main.py
GBM_WSSM_single_image.ipynb
GBM_WSSM_single_image.ipynb
Mask_Integer_Encoding.py
Mask_Integer_Encoding.py
Mask_Integer_Encoding_1.py
Mask_Integer_Encoding_1.py
Mask_Integer_Encoding_original.py
Mask_Integer_Encoding_original.py
Mask_Labels.txt
Mask_Labels.txt
NN_classification_MVP.py
NN_classification_MVP.py
RGB_color_picker.ijm
RGB_color_picker.ijm
blood_vessel_area_binning_analysis.R
blood_vessel_area_binning_analysis.R
blood_vessel_augmentations_may24.ipynb
blood_vessel_augmentations_may24.ipynb
blood_vessel_augmentations_may24.py
blood_vessel_augmentations_may24.py
blood_vessel_segmentation_augmented_data_may24.py
blood_vessel_segmentation_augmented_data_may24.py
bv_detect_210324.ijm
bv_detect_210324.ijm
check_GPU_resources.py
check_GPU_resources.py
check_img_data_format.py
check_img_data_format.py
check_segmentation_models.py
check_segmentation_models.py
classify_tumor_randomforest.py
classify_tumor_randomforest.py
classify_tumor_randomforest_updated.py
classify_tumor_randomforest_updated.py
create_blood_vessel_mask_deconv_110824.ijm
create_blood_vessel_mask_deconv_110824.ijm
create_classifier_from_annotations.groovy
create_classifier_from_annotations.groovy
create_margins_220324.groovy
create_margins_220324.groovy
create_tumor_margins.groovy
create_tumor_margins.groovy
deconvolute_macro.ijm
deconvolute_macro.ijm
deconvolute_multiplex_images.py
deconvolute_multiplex_images.py
demo_ml_script_020424.py
demo_ml_script_020424.py
demo_slurm_script_020424.sh
demo_slurm_script_020424.sh
detect_blood_vessel_190324.ijm
detect_blood_vessel_190324.ijm
detect_blood_vessel_210324.ijm
detect_blood_vessel_210324.ijm
detect_blood_vessel_230324.ijm
detect_blood_vessel_230324.ijm
detect_blood_vessel_240324.ijm
detect_blood_vessel_240324.ijm
extract_features.py
extract_features.py
extract_intensity_features_full_set3.py
extract_intensity_features_full_set3.py
extract_masks_from_images.ijm
extract_masks_from_images.ijm
extract_masks_from_one_image.ijm
extract_masks_from_one_image.ijm
final_3_cluster_LDA_analysis.R
final_3_cluster_LDA_analysis.R
images_augment_microvascular_proliferation.py
images_augment_microvascular_proliferation.py
images_processing_script.py
images_processing_script.py
iterate_over_roi_190324.ijm
iterate_over_roi_190324.ijm
label_image.py
label_image.py
label_image_with_border.py
label_image_with_border.py
label_image_with_border_updated.py
label_image_with_border_updated.py
modify_mask.py
modify_mask.py
predict_image_class.py
predict_image_class.py
predict_mask_segmentation_models.py
predict_mask_segmentation_models.py
qupath_script.groovy
qupath_script.groovy
run_RF_classifier.sh
run_RF_classifier.sh
run_base_models_GPU_local_env.sh
run_base_models_GPU_local_env.sh
run_check_gpu.sh
run_check_gpu.sh
run_check_gpu_modified.sh
run_check_gpu_modified.sh
run_mvp_albumentations.sh
run_mvp_albumentations.sh
run_nn_classify_CPU_local.sh
run_nn_classify_CPU_local.sh
run_nn_classify_mvp_GPU_local_env.sh
run_nn_classify_mvp_GPU_local_env.sh
run_optim_bs10_drp0_GPU_local_env.sh
run_optim_bs10_drp0_GPU_local_env.sh
run_optim_bs10_drp_all_GPU_local_env.sh
run_optim_bs10_drp_all_GPU_local_env.sh
run_optim_bs20_drp_all_GPU_local_env.sh
run_optim_bs20_drp_all_GPU_local_env.sh
run_optim_bs50_drp0_GPU_local_env.sh
run_optim_bs50_drp0_GPU_local_env.sh
run_optim_bs50_drp0_final_GPU_local_env.sh
run_optim_bs50_drp0_final_GPU_local_env.sh
run_optim_bs50_drp_all_GPU_local_env.sh
run_optim_bs50_drp_all_GPU_local_env.sh
run_predict_image_class.sh
run_predict_image_class.sh
run_segmentation.sh
run_segmentation.sh
run_segmentation_CPU.sh
run_segmentation_CPU.sh
run_segmentation_GPU_local_env.sh
run_segmentation_GPU_local_env.sh
run_segmentation_basic_gpu.sh
run_segmentation_basic_gpu.sh
run_segmentation_high_task.sh
run_segmentation_high_task.sh
run_sm_fpn_efficientnet_CPU_local.sh
run_sm_fpn_efficientnet_CPU_local.sh
run_sm_unet_efficientnet_2class_GPU_local_env.sh
run_sm_unet_efficientnet_2class_GPU_local_env.sh
run_unet_efficienet_b7_1024px_final_GPU_local_env.sh
run_unet_efficienet_b7_1024px_final_GPU_local_env.sh
run_unet_mvp_3layer_GPU_local_env.sh
run_unet_mvp_3layer_GPU_local_env.sh
run_unet_mvp_GPU_local_env.sh
run_unet_mvp_GPU_local_env.sh
run_unet_mvp_weights_GPU_local_env.sh
run_unet_mvp_weights_GPU_local_env.sh
run_utility_script1.sh
run_utility_script1.sh
segmentation_models_base_model.py
segmentation_models_base_model.py
select_object_by_objectID.groovy
select_object_by_objectID.groovy
select_object_by_objectID_updated.groovy
select_object_by_objectID_updated.groovy
sm_unet_eff_2_class_mvp_weights.py
sm_unet_eff_2_class_mvp_weights.py
sm_unet_eff_multiGPU.py
sm_unet_eff_multiGPU.py
sm_unet_effb7_3layer256_2class_mvp.py
sm_unet_effb7_3layer256_2class_mvp.py
sm_unet_effb7_3layer64_2class_mvp.py
sm_unet_effb7_3layer64_2class_mvp.py
sm_unet_efficientnet_2_class_1024px_FINAL.py
sm_unet_efficientnet_2_class_1024px_FINAL.py
sm_unet_efficientnet_2_class_FINAL.py
sm_unet_efficientnet_2_class_FINAL.py
sm_unet_efficientnet_2_class_bs10_drp0.py
sm_unet_efficientnet_2_class_bs10_drp0.py
sm_unet_efficientnet_2_class_bs10_drp2.py
sm_unet_efficientnet_2_class_bs10_drp2.py
sm_unet_efficientnet_2_class_bs10_drp3.py
sm_unet_efficientnet_2_class_bs10_drp3.py
sm_unet_efficientnet_2_class_bs10_drp5.py
sm_unet_efficientnet_2_class_bs10_drp5.py
sm_unet_efficientnet_2_class_bs20_drp0.py
sm_unet_efficientnet_2_class_bs20_drp0.py
sm_unet_efficientnet_2_class_bs20_drp2.py
sm_unet_efficientnet_2_class_bs20_drp2.py
sm_unet_efficientnet_2_class_bs20_drp3.py
sm_unet_efficientnet_2_class_bs20_drp3.py
sm_unet_efficientnet_2_class_bs20_drp5.py
sm_unet_efficientnet_2_class_bs20_drp5.py
sm_unet_efficientnet_2_class_bs50_drp0.py
sm_unet_efficientnet_2_class_bs50_drp0.py
sm_unet_efficientnet_2_class_bs50_drp2.py
sm_unet_efficientnet_2_class_bs50_drp2.py
sm_unet_efficientnet_2_class_bs50_drp3.py
sm_unet_efficientnet_2_class_bs50_drp3.py
sm_unet_efficientnet_2_class_bs50_drp5.py
sm_unet_efficientnet_2_class_bs50_drp5.py
sm_unet_efficientnet_aug_data_batch_size.py
sm_unet_efficientnet_aug_data_batch_size.py
tumor_normal_digital_brain_tumor_final.py
tumor_normal_digital_brain_tumor_final.py
tumor_normal_discriminate.ipynb
tumor_normal_discriminate.ipynb
unet_efficientnet_base_models.py
unet_efficientnet_base_models.py
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scripts for running blood vessel segmentation using pretrained models
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