Clean up codes before merge with master.

SBU-BMI · Jun 30, 2019 · bd0df89 · bd0df89
1 parent 86024f7
commit bd0df89
Show file tree

Hide file tree

Showing 542 changed files with 364 additions and 7,793 deletions.
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2019, Department of Biomedical Informatics
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -1,7 +1,20 @@
 # Nuclear image synthesis and segmentation code
 
-## Nuclear image synthesis
-training-data-synthesis
+This repository contains source code for the following paper:  
+Robust Histopathology Image Analysis: to Label or to Synthesize? Hou, Le and Agarwal, Ayush and Samaras, Dimitris and Kurc, Tahsin M and Gupta, Rajarsi R and Saltz, Joel H. Computer Vision and Pattern Recognition (CVPR), 2019  
 
-## Nuclei segmentation
-segmentation-tensorflow
+You need the following python2 libraries to run this software:  
+```
+tensorflow  
+scipy  
+numpy  
+json  
+pickle
+cv2 
+```
+
+If you want to obtain initial synthetic images with nuclear masks, please read training-data-synthesis/README.md  
+If you want to train your nuclei segmentation model, or use our trained nuclei segmentation model, please read segmentation-of-nuclei/README.md 
+
+This software uses several open source repositories, especially:  
+https://github.com/carpedm20/simulated-unsupervised-tensorflow
diff --git a/large_scale_training_testing/buffer.py b/large_scale_training_testing/buffer.py
diff --git a/large_scale_training_testing/clear.sh b/large_scale_training_testing/clear.sh
diff --git a/large_scale_training_testing/data/utils.py b/large_scale_training_testing/data/utils.py
diff --git a/large_scale_training_testing/run_train.sh b/large_scale_training_testing/run_train.sh
diff --git a/large_scale_training_testing/run_wsi_seg.sh b/large_scale_training_testing/run_wsi_seg.sh
diff --git a/real-training-data-extraction/README.md b/real-training-data-extraction/README.md
diff --git a/real-training-data-extraction/extract_all.py b/real-training-data-extraction/extract_all.py
diff --git a/real-training-data-extraction/extract_all.sh b/real-training-data-extraction/extract_all.sh
diff --git a/real-training-data-extraction/extract_patches_a_dataset_and.py b/real-training-data-extraction/extract_patches_a_dataset_and.py