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Title: GitHub - DIDSR/dldp · GitHub

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Description: Contribute to DIDSR/dldp development by creating an account on GitHub.

Open Graph Description: Contribute to DIDSR/dldp development by creating an account on GitHub.

X Description: Contribute to DIDSR/dldp development by creating an account on GitHub.

Opengraph URL: https://github.com/DIDSR/dldp

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LICENSE.mdhttps://github.com/DIDSR/dldp/blob/master/LICENSE.md
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README.mdhttps://github.com/DIDSR/dldp/blob/master/README.md
README.mdhttps://github.com/DIDSR/dldp/blob/master/README.md
requirements.txthttps://github.com/DIDSR/dldp/blob/master/requirements.txt
requirements.txthttps://github.com/DIDSR/dldp/blob/master/requirements.txt
setup.pyhttps://github.com/DIDSR/dldp/blob/master/setup.py
setup.pyhttps://github.com/DIDSR/dldp/blob/master/setup.py
READMEhttps://github.com/DIDSR/dldp
Licensehttps://github.com/DIDSR/dldp
https://github.com/DIDSR/dldp#deep-learning-for-digital-pathology-dldp---camelyon-2016-dataset
https://github.com/3dimaging/Accessory/blob/master/workflow2.png
https://github.com/DIDSR/dldp
https://github.com/DIDSR/dldp#code-overview
https://github.com/3dimaging/Accessory/blob/master/pipeline.png
Training image extractionhttps://github.com/DIDSR/dldp/tree/master/dldp/patch_extract
Image processinghttps://github.com/DIDSR/dldp/tree/master/dldp/image_process
Neural network traininghttps://github.com/DIDSR/dldp/tree/master/dldp/cnn_train
Heatmap constructionhttps://github.com/DIDSR/dldp/tree/master/dldp/heatmap_pred
Slide-based predictionhttps://github.com/DIDSR/dldp/tree/master/dldp/model_eva/roc
Lesion-based predictionhttps://github.com/DIDSR/dldp/tree/master/dldp/model_eva/froc
WSI-heatmap visualizationhttps://github.com/DIDSR/dldp/tree/master/dldp/wsi_visu
Code Documentationhttps://github.com/DIDSR/dldp/blob/master/docs/build/html/index.html
https://github.com/DIDSR/dldp#0---preparation
https://github.com/DIDSR/dldp#01-set-up-deep-learning-environment
Setup Python Environmenthttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/requirements.txt
Package Installation for Color Normalizationhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/Color_Normalization.md
https://github.com/DIDSR/dldp#02-asap-installation-and-image-display
https://github.com/DIDSR/dldp#openslide
OpenSlide Installationhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/OpenSlide_Installation.md
https://github.com/3dimaging/Accessory/blob/master/webserver.png
https://github.com/3dimaging/Accessory/blob/master/webserver-enlarged.png
https://github.com/DIDSR/dldp#asap
ASAP Installationhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/ASAP_installation.txt
https://github.com/DIDSR/dldp#03-mask-image-generation
Camelyon 17 websitehttps://camelyon17.grand-challenge.org/Data/
Code for Mask file generation - for training (tumor) WSIshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/mask_generation_asap.py
Code for Mask file generation - for testing (tumor) WSIshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/xml_to_mask.py
https://github.com/3dimaging/Accessory/blob/master/389e2c0cd56cf3ea1356fd03a2af35cc-94048Vj0.png
https://github.com/DIDSR/dldp#04-data-description-important
CAMELYON16 Data Sethttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/Camelyon16_dataset_description.md
https://github.com/DIDSR/dldp#05---wsi-visulization-with-annotation
https://github.com/DIDSR/dldp#annotation-visulization
https://github.com/3dimaging/Accessory/blob/master/annotation%20over%20wsi.png
https://github.com/DIDSR/dldp#2---image-processing
https://github.com/DIDSR/dldp#21-image-segmentation
https://github.com/DIDSR/dldp#22-patch-extraction
Extract normal image patches from normal slideshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/patch_extract/Extract_Normal_Patches_From_Normal_Slides.py
Extract normal and tumor image patches from tumor slideshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/patch_extract/Extract_Normal_and_Tumor_Patches_From_Tumor_Slides.py
https://github.com/DIDSR/dldp#step-0--tumor-training-images-and-normal-training-images-were-randomly-divided-into-training-and-validation-data-set
https://github.com/DIDSR/dldp#step-1--randomly-extract-patches-256-x-256-on-the-tissue-region-at-the-level-of-40x
https://github.com/DIDSR/dldp#step-2--crop-224x224-patches-and-conduct-image-augmentation
flip, rotation and croppinghttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/image_process/patch_aug.py
https://github.com/3dimaging/Accessory/blob/master/crop%20and%20flip.png
Stain (color) normalizationhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/image_process/color_normalization.py
https://github.com/3dimaging/Accessory/blob/master/color%20variety.png
https://github.com/3dimaging/Accessory/blob/master/color_norm2.png
Adding color noisehttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/image_process/patch_aug.py
https://github.com/3dimaging/Accessory/blob/master/dayong_addingcolornoise_HSV.png
https://github.com/3dimaging/Accessory/blob/master/dayong_addingcolornoise_rgb.png
https://github.com/3dimaging/Accessory/blob/master/color_pertubation_liu_yun_1.png
https://github.com/3dimaging/Accessory/blob/master/color_perturbation_liu_yun_2.png
Image Generatorhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/cnn_train/Training_Patch_Pre.py
https://github.com/DIDSR/dldp#step-3--image-generator
https://github.com/3dimaging/Accessory/blob/master/patches.png
https://github.com/3dimaging/Accessory/blob/master/patche%20ground%20truth.png
https://github.com/DIDSR/dldp#3---training-neural-network
https://github.com/DIDSR/dldp#flowchart-for-model-training-and-prediction
https://github.com/3dimaging/Accessory/blob/master/workflow%20for%20model%20training.png
https://github.com/DIDSR/dldp#googlenet-inception-v1-training
https://github.com/DIDSR/dldp#step-1-network-training
Training GoogleNethttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/cnn_train/main.py
https://github.com/DIDSR/dldp#step-2-hard-negative-mining
Extract False Positive Patcheshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/image_process/main_pred_hnm_workstation.py
https://github.com/DIDSR/dldp#extract-false-positive-patches
https://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/patch_index.pyhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/patch_index.py
A HPC version is availablehttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/main_pred_hnm_hpc.py
https://github.com/3dimaging/Accessory/blob/master/false%20positive%20patches.png
https://github.com/3dimaging/Accessory/blob/master/wrong%20predicted%20patches.png
https://github.com/DIDSR/dldp#neural-network-training-with-false-positive-patches
the same codehttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/cnn_train/main.py
https://github.com/DIDSR/dldp#step-3-neural-network-training-with-false-positive-patches-and-normal-patches-near-tumor-regions
Extract Normal Patches Near Tumor Regionshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/image_process/patches_near_tumor.py
https://github.com/DIDSR/dldp#extract-normal-patches-near-tumor-regions
https://github.com/DIDSR/dldp#neural-network-training-with-false-positive-patches-and-normal-patches-near-tumor-regions
the same codehttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/cnn_train/main.py
https://github.com/DIDSR/dldp#4---prediction-and-evaluation
https://github.com/DIDSR/dldp#41-make-predictions-and-heatmap-stitching
https://github.com/3dimaging/Accessory/blob/master/HPC_new.png
patch_index.py in utilshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/utils/patch_index.py
Code for prediction - slide window - googlenet - HPC versionhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/Pred_Slide_Window_For_Heatmap_main.py
Code for prediction - slide window - googlenet - Workstation versionhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/Pred_Slide_Window_For_Heatmap_main_workstation.py
code for heatmap stitching - HPC versionhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/Heat_Map_Build0319_betsy.py
code for heatmap stitching - Workstation versionhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/Heat_Map_Build0319_workstation.py
https://github.com/DIDSR/dldp#heatmap-examples-from-googlenet-prediction-only
https://github.com/3dimaging/Accessory/blob/master/test_075.png
https://github.com/3dimaging/Accessory/blob/master/test_073.png
https://github.com/3dimaging/Accessory/blob/master/49285XZv.png
https://github.com/DIDSR/dldp#if-some-tasks-on-hpc-fail
find the failed taskshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/task_id_remained.py
https://github.com/DIDSR/dldp#step-1-find-the-failed-tasks
redo the failed taskshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/task_id_makeup.py
https://github.com/DIDSR/dldp#step-2-redo-the-failed-tasks
copy the resultshttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/heatmap_pred/copy_makeup_files.py
https://github.com/DIDSR/dldp#step-3-copy-the-results
https://github.com/DIDSR/dldp#42a-slide-based-classification
Extracting Features from Heatmaps for Whole-slide Image Classificationhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/model_eva/roc/Parameter_Extraction_For_Random_Forest_Batch.py
https://github.com/DIDSR/dldp#extracting-features-from-heatmaps-for-whole-slide-image-classification
https://github.com/DIDSR/dldp#global-features-extraction
https://github.com/DIDSR/dldp#local-features-extraction
https://github.com/DIDSR/dldp#results
https://github.com/3dimaging/Accessory/blob/master/feature%20extraction.png
Random Forest Training and Testinghttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/model_eva/roc/RF_training_batch.py
https://github.com/DIDSR/dldp#random-forest-training-and-testing
https://github.com/DIDSR/dldp#important-features
https://github.com/3dimaging/Accessory/blob/master/important%20features.png
https://github.com/DIDSR/dldp#42b-lesion-based-detection
Lesion-based detectionhttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/model_eva/froc/FROC_csv_0604.py
https://github.com/DIDSR/dldp#43-roc-and-froc-generation
https://github.com/DIDSR/dldp#roc
https://github.com/3dimaging/Accessory/blob/master/ROC.png
python scripthttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/model_eva/roc/RF_training_batch.py
Code for AUChttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/model_eva/roc/script_auc.R
https://github.com/DIDSR/dldp#froc
Code for FROChttps://github.com/DIDSR/DeepLearningCamelyon/blob/master/dldp/dldp/model_eva/froc/FROC_Calcu_with_home_made_mask.py
https://github.com/3dimaging/Accessory/blob/master/FROC.png
https://github.com/DIDSR/dldp#references
https://arxiv.org/abs/1606.05718https://arxiv.org/abs/1606.05718
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820737/?report=reader#!po=59.4340https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820737/?report=reader#!po=59.4340
https://academic.oup.com/gigascience/article/7/6/giy065/5026175https://academic.oup.com/gigascience/article/7/6/giy065/5026175
Readme https://github.com/DIDSR/dldp#readme-ov-file
View license https://github.com/DIDSR/dldp#License-1-ov-file
Please reload this pagehttps://github.com/DIDSR/dldp
Activityhttps://github.com/DIDSR/dldp/activity
Custom propertieshttps://github.com/DIDSR/dldp/custom-properties
1 forkhttps://github.com/DIDSR/dldp/forks
Report repository https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FDIDSR%2Fdldp&report=DIDSR+%28user%29
Releaseshttps://github.com/DIDSR/dldp/releases
Packages 0https://github.com/orgs/DIDSR/packages?repo_name=dldp
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Contributorshttps://github.com/DIDSR/dldp/graphs/contributors
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Python 92.0% https://github.com/DIDSR/dldp/search?l=python
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