Update README.md

README.md

@@ -4,13 +4,19 @@ pipeline_tag: image-segmentation
 tags:
 - medical
 - biology
-- histology
 ---
 
-# Cellpose Nuclei Segmentation Model Trained With High Grade Serous Ovarian Cancer Dataset!
+# Cellpose Model for High-Grade Serous Ovarian Cancer Nuclei Segmentation
 
+## Dataset
+Semi-manually annotated HGSC Primary Omental samples from the (private) DECIDER cohort. Data acquired in the DECIDER project, 
+funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 965193.
 
-# Dataset classes
+**Contains:**
+- 198 varying sized image crops at 20x magnification.
+- 98 468 annotated nuclei
+
+## Dataset classes
 
 ```
 nuclei_classes = {
@@ -24,6 +30,14 @@ nuclei_classes = {
 }
 ```
 
+## Dataset Class Distribution
+- connective nuclei: 46 100 (~47%)
+- neoplastic nuclei: 22 761 (~23%)
+- inflammatory nuclei 19 185 (~19%)
+- dead nuclei 1859 (~2%)
+- macrophage nuclei and cytoplasms: 4550 (~5%)
+
+# USAGE
 
 ## 1. Install cellseg_models.pytorch and albumentations
 ```
@@ -94,7 +108,12 @@ ax[1].imshow(label2rgb(out["nuc"][0][0], bg_label=0)) # inst_map
 ax[2].imshow(label2rgb(out["nuc"][0][1], bg_label=0)) # type_map
 ```
 
-## Citation
+# Model Training Details:
+First, the image crops in the training data were tiled into 224x224px patches with a sliding window (stride=32px). 
+
+Rest of the training procedures follow this notebook: [link]
+
+# Citation
 
 cellseg_models.pytorch:
 ```
@@ -137,5 +156,4 @@ Unless required by applicable law or agreed to in writing, software distributed
 ## Additional Terms
 
 While the Apache 2.0 License grants broad permissions, we kindly request that users adhere to the following guidelines:
-Medical or Clinical Use: This model is not intended for use in medical diagnosis, treatment, or prevention of disease of real patients. It should not be used as a substitute for professional medical advice.
-
+Medical or Clinical Use: This model is not intended for use in medical diagnosis, treatment, or prevention of disease of real patients. It should not be used as a substitute for professional medical advice.