====== WELCOME to the Crary Lab Slide Wiki! ======

The Crary Lab Slide Wiki serves as a centralized hub for organizing, accessing, and sharing information about our slide-based research and neuropathological studies. This platform is designed to streamline collaboration, foster knowledge exchange, and ensure that valuable insights and resources are readily available to all members of the lab.

===== Purpose of This Wiki =====
  * To document and share protocols, methods, and findings related to neuropathology and neurodegenerative diseases.
  * To provide detailed descriptions and annotations for slides and associated data.
  * To serve as a dynamic resource for onboarding new lab members and keeping everyone updated on ongoing projects.
  * To enable seamless collaboration by consolidating lab resources in one easily accessible location.

===== Getting Started =====
  * Use the **navigation menu** to browse through available pages and topics.
  * Check out the **protocols** section for step-by-step guides and reference materials.
  * Visit the **resources** page for links to key datasets, papers, and tools.
  * Need help or have questions? Head over to the **FAQ** or contact a team member.

Together, let’s make this wiki a living resource for collaboration, discovery, and innovation! 

==== CONTENTS ====

===== Standard Operating Protocols =====
  * [[sops:slide_preparation|Slide Preparation]]
  * [[sops:staining|Staining Procedures]]
  * [[sops:mounting|Slide Mounting Protocols]]
  * [[sops:Slide_Scanning|Imaging and Scanning]]
  * [[sops:Slide_data_management|Data Management and Archiving]]
  * [[sops:DSA|Digital Slide Archive]]
  * [[sops:Annotating_Slides|Slide Annotation]]
  * [[sops:Data_Security |Data Security]]
  * [[sops:lab_safety|Lab Safety Guidelines]]
  * [[sops:faq|SOP FAQ]]

===== Cohorts =====
  * [[cohorts:overview|Cohort Overview]]
  * [[cohorts:alzheimers|Alzheimer’s Disease Cohort]]
  * [[cohorts:cte|Chronic Traumatic Encephalopathy (CTE) Cohort]]
  * [[cohorts:psp|Progressive Supranuclear Palsy (PSP) Cohort]]
  * [[cohorts:control|Control Cohort]]
  * [[cohorts:metadata|Clinical Metadata and Recruitment]]
  * [[cohorts:faq|Cohort FAQ]]

===== Collections =====
  * [[collections:overview|Collections Overview]]
  * [[collections:histological|Histological Slide Collections]]
  * [[collections:digital|Digital Slide Collections]]
  * [[collections:archived|Archived Slides]]
  * [[collections:metadata_templates|Metadata Templates]]
  * [[collections:retrieval|Slide Retrieval Procedures]]
  * [[collections:faq|Collections FAQ]]

===== Projects =====
  * [[projects:overview|Project Overview]]
  * [[projects:braak_staging|Braak Staging Correlation with Clinical Data]]
  * [[projects:tau_cte|Tau Pathologyin CTE]]
  * [[projects:Atrophy|Atrophy Project]]
  * [[projects:biomarkers|Imaging Biomarker Development]]
  * [[projects:Genetics|Genetic Correlations with Neurodegenerative Disease Development]]
  * [[projects:HistoAge|Histoage Project]]
  * [[projects:Organoids|Organoids Project]]
  * [[projects:Hippocampal_Segmentation|Hippocampal SegmentationProject]]
  * [[projects:Foundation_Model|Foundation Model 1.0]]
  * [[projects:Git_hub_development|Crary Lab Github Devops]]
  * [[projects:completed|Completed Projects]]
  * [[projects:proposed|Proposed Projects and Ideas]]
  * [[projects:collaboration|Collaboration and External Partners]]
  * [[projects:faq|Projects FAQ]]

===== Resources =====
  * [[resources:tools|Tools and Software]]
  * [[resources:Digital_Slide_archive| https://crarylabslides.com | DSA Link]]
  * [[resources:datasets|Internal and Public Datasets]]
  * [[resources:publications|Lab Publications]]
  * [[resources:partnerships|Collaborators and Partnerships]]
  * [[resources:access_guides|Access Guides and Login Help]]
  * [[resources:faq|Resources FAQ]]

===== FAQ =====
  * [[faq:general|General FAQ]]
  * [[faq:technical|Technical Issues]]
  * [[faq:troubleshooting|Troubleshooting Guide]]
  * [[faq:contact|Contact Information]]