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Welcome to the 𝑓(Cell) wiki!

Introduction:

This software will always be open source, and available to any researcher using it for non-profit work. For the moment, the software is designed around intensity-based optoretinography, or iORG processing. That means that it is capable of processing/analyzing data from any en-face device that produces videos, such as scanning laser ophthalmoscopes or line-scan ophthalmoscopes, and their adaptive optics variants (e.g. AO-SLO/AO-LSO/AO-FiO).

This wiki in particular is designed to help with the creation of configuration files, as well as provide explanations to the variety of configuration options available to a user. If you're just looking to "get up and go", see the Quick Start page. Otherwise, keep reading, and see how deep the rabbit hole goes...

General Flow Diagram:

Currently, 𝑓(Cell) performs its analyses in the following stages; only the required stages are shown.

flowchart LR

    subgraph preanalysis["Pre-Analysis Pipeline"]
        direction TB
    AA(Load Dataset) --> BB([Parse Tags/Metadata])
    BB([Parse Tags/Metadata]) --> HH([Intra-Video Torsion Removal])
    HH([Intra-Video Torsion Removal]) --> II(Data Output and Sorting)
    end

    preanalysis --> analysis

    subgraph analysis["Analysis"]
        direction TB
    A(Load Dataset) --> B([Parse Tags/Metadata])
    B([Parse Tags/Metadata])  --> D([Segment Query Points / Extract ORGs])
    D([Segment Query Points / Extract ORG])  --> E([Standardize ORGs])
    E([Standardize ORGs])  --> F([Summarize ORGs])
    end
    
    click BB "https://github.com/OCVL/F-Cell/wiki/Advanced:-Tag-Parsing" "Tag Parsing"
    click CC "https://github.com/OCVL/F-Cell/wiki/Advanced:-Pre%E2%80%90Analysis-Pipeline#general-parameters" "Custom Steps"
    click DD "https://github.com/OCVL/F-Cell/wiki/Advanced:-Pre%E2%80%90Analysis-Pipeline#trimming" "Trim Video"
    click EE "https://github.com/OCVL/F-Cell/wiki/Advanced:-Pre%E2%80%90Analysis-Pipeline#flat-fielding" "Flat Field"
    click FF "https://github.com/OCVL/F-Cell/wiki/Advanced:-Pre%E2%80%90Analysis-Pipeline#blurring" "Blurring"
    click GG "https://github.com/OCVL/F-Cell/wiki/Advanced:-Pre%E2%80%90Analysis-Pipeline#roi-masking" "Crop Video"
    click HH "https://github.com/OCVL/F-Cell/wiki/Advanced:-Pre%E2%80%90Analysis-Pipeline#torsion-correction" "Intra-Video Torsion Removal"

    click B "https://github.com/OCVL/F-Cell/wiki/Advanced:-Tag-Parsing" "Tag Parsing"
    click C "https://github.com/OCVL/F-Cell/wiki/Advanced:-Analysis-Parameters#data-normalization" "Normalize Data"
    click D "https://github.com/OCVL/F-Cell/wiki/Advanced:-Analysis-Parameters#query-point-segmentation" "Query Point Segmentation"
    click E "https://github.com/OCVL/F-Cell/wiki/Advanced:-Analysis-Parameters#signal-standardization" "Standardization"
    click F "https://github.com/OCVL/F-Cell/wiki/Advanced:-Analysis-Parameters#org-summary" "Summarization"
    click G "https://github.com/OCVL/F-Cell/wiki/Advanced:-Analysis-Metrics" "Metrics"
    click H "https://github.com/OCVL/F-Cell/wiki/Advanced:-Analysis-Display-Parameters" "Display Results"

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