first commit

Author: jack-mcmahon

README.md

@@ -1,9 +1,31 @@
-# Project Name
+# GramViT 
 
-## Contents
+The repo contains the trained model and code for the paper, [A Novel Framework for the Automated Characterization of Gram Stained Blood Culture Slides Using a Large Scale Vision Transformer](https://pages.github.com/). GramViT is a region-sampling framework for characterizing Gram-stained slides using Microsoft's LongViT vision Transformer model.
+
+Our model was trained to characterize five common categories of Gram-stained WSIs: Gram-positive cocci in clusters, Gram-positive cocci in pairs/chains, Gram-positive rods, Gram-negative rods, and slides with no bacteria. It was trained using a 475-slide dataset of blood culture Gram-stained slides collected at Dartmouth Hitchcock Medical Center (Lebanon, New Hampshire, USA).
+
+![Model figure](GramViT/figures/gramvit.png)
 
 ## Dependencies
 
+See requirements.txt
+
 ## Usage
 
-## Citations
+In order to use this repository, you need to create a cvs file for your dataset containing dataset metadata and file paths.
+
+1: Extract regions from each svs file
+
+    python preprocessing/1_get_regions.py --csv_file_path --output_folder --region_size
+
+2: Build Dataset Index
+
+    python preprocessing/2_create_index.py --index_path --pickle_split_path --total_fold
+
+3: Train Model 
+
+    bash code/launch_finetuning_gs.py
+
+4: Evaluate Model
+
+    bash code/launch_evaluate_gs_finetune.py