Advanced

Advanced configuration information.

This portion of the wiki contains the full specification information for the 𝑓(Cell) JSON, and is recommended for experienced programmers or scrappy adventurers.

Below are all possible steps for both the pre-analysis and analysis stages of F(Cell), where optional stages are indicated with dashed lines.

flowchart LR

    subgraph preanalysis["Pre-Analysis Pipeline"]
        direction TB
    AA(Load Dataset) --> BB([Parse Tags/Metadata])
    BB([Parse Tags/Metadata]) --> CC([Perform Custom Steps]) 
    CC([Perform Custom Steps]) --> DD([Trim Video]) 
    DD([Trim Video]) --> EE([Flat Field]) 
    EE([Flat Field]) --> FF([Gaussian Blur]) 
    FF([Gaussian Blur]) --> GG([Crop Video]) 
    GG([Crop Video]) --> 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])  --> Ba([Gaussian Blur])
    Ba([Gaussian Blur])  --> C([Normalize Dataset])
    C([Normalize Dataset])  --> D([Segment Query Points / Extract ORGs])
    D([Segment Query Points / Extract ORG])  --> E([Standardize ORGs])
    E([Standardize ORGs])  --> F([Summarize ORGs])
    F([Summarize ORGs])  --> G([Extract Metrics])
    G([Extract Metrics])  --> H(Display/Output Results)
    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"

    classDef optional stroke-dasharray:4 5;
    class CC,DD,EE,FF,GG optional;

    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"

    class Ba,C,G,H optional;

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