Merge pull request #84 from DIDSR/dev

publications reordering and disclaimer added

assets/pages/disclaimer.md

@@ -0,0 +1,8 @@
+---
+layout: page
+title: Commercial Products Disclaimer
+---
+
+The mention of commercial products, their sources, or their use in connection with material reported herein is not to be construed as either an actual or implied endorsement of such products by the Department of Health and Human Services. This website is a contribution of the U.S. Food and Drug Administration and is not subject to copyright.
+
+If you have any questions regarding this, please reach out to [the team.](./team.md)

assets/pages/process-guides/caMicro-ProcessGuide-ROIselection.md

@@ -27,25 +27,27 @@ The overarching goal of ROI selection is to perform a first pass assessment of a
 
 5. Select **10 ROIs** per WSI. Any tissue in the WSI is eligible for annotation. However, we aim to create a diverse set of ROIs which contains both anomalies, such as pitfalls and artifacts, as well as high-value sTILs densities. Therefore: **target diverse morphology and sTILs density** (especially high sTILs density) while distributing ROIs across entire tissue. Each ROI can satisfy multiple targets. Not all targets can be satisfied in each WSI. The numbers to select mentioned below are guides. 
 
-In each WSI:  
+    In each WSI:  
 
-**a.**  Select 3 ROIs inside tumor with stroma    
+    **a.**  Select 3 ROIs inside tumor with stroma    
 
- (1 ROI should be at least 25% void of tissue)    
+     (1 ROI should be at least 25% void of tissue)    
 
-**b.**  Select 2 ROIs at invasive margin if discernable with stroma   
+    **b.**  Select 2 ROIs at invasive margin if discernable with stroma   
 
- (not sure this is possible with biopsies, 1 ROI should be at least 25% void of tissue)   
+     (not sure this is possible with biopsies, 1 ROI should be at least 25% void of tissue)   
 
-**c.**  Select 2 ROIs inside tumor or at margin **without stroma**
+    **c.**  Select 2 ROIs inside tumor or at margin **without stroma**
 
- (not sure there are many or any of these)    
+     (not sure there are many or any of these)    
 
-**d.**  Select 2 ROIs where there is no proximal tumor   
+    **d.**  Select 2 ROIs where there is no proximal tumor   
+
+     (normal tissue: outside 500 μm tumor margin)
+
+    **e.**  Select 2 ROIs for each for the 16 pitfalls listed. The pitfalls were identified during sessions to understand pathologist variability and improve pathologist training and instructions for the assessment of sTILs [(Garcia2022_Cancers_v14p2467)](https://doi.org/10.3390/cancers14102467). The pitfalls are discussed and exemplified in the [CME course](../training-2023/cmeCourse.md), the test with feedback, and the [reference document](../training-2023/feedbackRefDoc.md). 
 
- (normal tissue: outside 500 μm tumor margin)
 
-**e.**  Select 2 ROIs for each for the 16 pitfalls listed. The pitfalls were identified during sessions to understand pathologist variability and improve pathologist training and instructions for the assessment of sTILs [(Garcia2022_Cancers_v14p2467)](https://doi.org/10.3390/cancers14102467). The pitfalls are discussed and exemplified in the [CME course](../training-2023/cmeCourse.md), the test with feedback, and the [reference document](../training-2023/feedbackRefDoc.md). 
 
 6. Provide Annotations on selected ROIs.  HTT sTILs Study Annotations collected:   
 
@@ -80,6 +82,8 @@ In each WSI:
 
 ## Pitfalls
 
+Part 3 of the [CME course slides](../training-2023/pdfs/cmeCourseSlides-combined-final-20230217.pdf) offers visual examples of each type of pitfall you might find.
+
 | benign glandular elements	| cross-sectionally cut fibroblasts | 
 | adipocytes | low grade and/or degenerate ischemic tumor cells | 
 | carcinoma in situ | crushed cells | 

assets/pages/publications.md

@@ -8,20 +8,21 @@ title: HTT Publications
 **Manuscript describing our MDDT process:**
  [S. Hart et al., “Initial interactions with the FDA on developing a validation dataset as a medical device development tool,” J Pathol, p. path.6208, Oct. 2023](https://doi.org/10.1002/path.6208)
 
-**Video presentation giving an overview of the project:**
- [Developing a dataset to validate computational models that analyze digital pathology images to assess TILs in breast cancer on Vimeo](https://vimeo.com/767440412)
-
-**Manuscript describing the project:**
- [Dudgeon et al. (2020), "A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study," Journal of Pathology Informatics, 12, p. 45](https://www.doi.org/10.4103/jpi.jpi_83_20)
+**Manuscript describing pilot study results:**
+ [Elfer et al. (2022), “Pilot study to evaluate tools to collect pathologist annotations for validating machine learning algorithms,” J. Med. Imag., 9, p. 047501](https://www.doi.org/10.1117/1.JMI.9.4.047501)
 
 **Manuscript describing expert panel based on pilot study:**
  [Garcia et al. (2022), “Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer,” Cancers, 14, p. 2467](https://www.doi.org/10.3390/cancers14102467)
 
-**Manuscript describing pilot study results:**
- [Elfer et al. (2022), “Pilot study to evaluate tools to collect pathologist annotations for validating machine learning algorithms,” J. Med. Imag., 9, p. 047501](https://www.doi.org/10.1117/1.JMI.9.4.047501)
-
 **Manuscript about Multi-reader Multi-case Analysis of Limits of Agreement:**
  [Wen and Gallas (2022), “Three-Way Mixed Effect ANOVA to Estimate MRMC Limits of Agreement,” Stat Biopharm Res, p. 1–10](https://www.doi.org/10.1080/19466315.2022.2063169)
 
+**Video presentation giving an overview of the project:**
+ [Developing a dataset to validate computational models that analyze digital pathology images to assess TILs in breast cancer on Vimeo (2022)](https://vimeo.com/767440412)
+
+**Manuscript describing the project:**
+ [Dudgeon et al. (2020), "A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study," Journal of Pathology Informatics, 12, p. 45](https://www.doi.org/10.4103/jpi.jpi_83_20)
+
+
 ## Full Library of Work from the HTT Team
 [HTT Zotero library](https://www.zotero.org/groups/4384613/eedap_studies_presentations_publications_and_studies/library)

index.html

@@ -12,6 +12,7 @@ <h2><strong>Key Pages</strong></h2>
             <li><a href="./assets/pages/training-2023">Training Materials</a></li>
             <li><a href="./assets/pages/pivotal-study">Pivotal Study</a></li>
             <li><a href="./assets/pages/publications">Publications</a></li>
+            <li><a href= "./assets/pages/disclaimer">Commercial Products Disclaimer</a></li>
         </ul>
     </menu>