Merge branch 'master' into dev

README.md

@@ -16,7 +16,7 @@ Imaging datasets in cancer research are growing exponentially in both quantity a
 
     docker pull pathml/pathml && docker run -it -p 8888:8888 pathml/pathml
 
-Done, what analyses can I write now? 👉 <kbd> <br> **[🔬🤖 Click here to launch your PathML Digital Pathology Assistant 🎓](https://chat.openai.com/g/g-L1IbnIIVt-digital-pathology-assistant-v3-0)** <br> </kbd>
+Done, what analyses can I write now? 👉 <a href="https://chat.openai.com/g/g-L1IbnIIVt-digital-pathology-assistant-v3-0" target="_blank"><img src="https://github.com/Dana-Farber-AIOS/pathml/assets/25375373/7fdc35b4-fede-431b-a8d5-324bea1873e4" width="30%"/></a>
 
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ai-digital-pathology-assistant-v3/README.md

@@ -24,7 +24,7 @@ It will help you:
 
 ## Recreate it
 
-[Here](./src) you will find all material needed to re-create our Digital Pathology Assistant, which is a custom OpenAI GPT available to all ChatGPT Plus users for research purposes. 
+[Here](./src) you will find all material needed to re-create our Digital Pathology Assistant, which is a custom OpenAI GPT available to all ChatGPT Pro users for research purposes. 
 
 ## Note 
 

examples/README.md

@@ -0,0 +1,16 @@
+# Examples of PathML usage
+
+These examples assume you are all set with ``PathML`` installation, let's get started with some analyses you can easily replicate:
+
+        
+1. [Load over 160+ different types of pathology images using PathML](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/loading_images_vignette.ipynb)
+2. [H&E Stain Deconvolution and Color Normalization](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/stain_normalization.ipynb)
+3. [Brightfield imaging pipeline: load an image, preprocess it on a local cluster, and get it read for machine learning analyses in PyTorch](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/workflow_HE_vignette.ipynb)
+4. [Multiparametric Imaging: Quickstart & single-cell quantification](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/multiplex_if.ipynb)
+5. [Multiparametric Imaging: CODEX & nuclei quantization](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/codex.ipynb)
+6. [Train HoVer-Net model to perform nucleus detection and classification, using data from PanNuke dataset](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/train_hovernet.ipynb)
+7. [Gallery of PathML preprocessing and transformations](https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/pathml_gallery.ipynb)
+8. Other examples from the [Rosenthal et al. 2022 paper](https://aacrjournals.org/mcr/article/20/2/202/678062/Building-Tools-for-Machine-Learning-and-Artificial) can be found in the [`vignettes`](https://github.com/Dana-Farber-AIOS/pathml/tree/master/examples/vignettes) folder 
+
+<img src="https://github.com/Dana-Farber-AIOS/pathml/assets/25375373/502c9e69-e988-4d61-b50f-0d6bfc8af251" width="1000px" />
+