Workflow

This section gives a broad overview of the steps taken in processing images.

Topotracing : Processing a single .spm file

Topotracing loads images from .spm files and extracts the specified channel, performing various filtering stages (Filters() class) before finding grains (Grains() class) and then calculating statistics for each grain (GrainStats() class). The Gaussian filtered image and labelling of grains is then passed onto DNA Tracing.

        %%{init: {'theme': 'base',
         }
}%%
graph TD;

  subgraph Background Flattening
  A1([Load YAML Configuration]) --> A2([Load SPM])
  A2 --> A3([Extract channel from SPM])
  A3 --> A4([Initial Align])
  A4 --> A5([Initial Tilt Removal])
  A5 --> A6([Thresholding Otsu])
  A6 --> A7([Mask Generation])
  A7 --> A8([Masked Align])
  A8 --> A9([Masked Tilt Removal])
  A9 --> A10([Background Zeroing])
  end
  subgraph Grain Finding
  A10 --> B1([Lower Thresholding])
  B1 --> B2([Gaussian Filtering])
  B2 --> B3([Tidy Edges])
  B3 --> B4([Preliminary Statistics])
  B4 --> B5([Size Thresholding])
  B5 --> B6([Label Regions])
  end
  subgraph Grain Statistics
  B6 --> C2([Calculate Points])
  C2 --> C8([Height & Volume Statistics])
  C2 --> C3([Calculate Edges])
  C2 --> C4([Calculate Centroid])
  C3 --> C5([Calculate Radius Statistics])
  C3 --> C6([Convex Hull / Graham Scan])
  C6 --> C7([Minimum Bounding Box Statistics])
  end
  subgraph DNA Tracing
  B2 --> D1([More Analysis])
  B5 --> D1
  end
  style A1 fill:#648FFF,stroke:#000000
  style A2 fill:#648FFF,stroke:#000000
  style A3 fill:#648FFF,stroke:#000000
  style A4 fill:#648FFF,stroke:#000000
  style A5 fill:#648FFF,stroke:#000000
  style A6 fill:#648FFF,stroke:#000000
  style A7 fill:#648FFF,stroke:#000000
  style A8 fill:#648FFF,stroke:#000000
  style A9 fill:#648FFF,stroke:#000000
  style A10 fill:#648FFF,stroke:#000000
  style B1 fill:#DC267F,stroke:#000000
  style B2 fill:#DC267F,stroke:#000000
  style B3 fill:#DC267F,stroke:#000000
  style B4 fill:#DC267F,stroke:#000000
  style B5 fill:#DC267F,stroke:#000000
  style B6 fill:#DC267F,stroke:#000000
  style C2 fill:#FE6100,stroke:#000000
  style C3 fill:#FE6100,stroke:#000000
  style C4 fill:#FE6100,stroke:#000000
  style C5 fill:#FE6100,stroke:#000000
  style C6 fill:#FE6100,stroke:#000000
  style C7 fill:#FE6100,stroke:#000000
  style C8 fill:#FE6100,stroke:#000000
  style D1 fill:#785EF0,stroke:#000000
    

DNA Tracing : Processing a single grain

        %%{init: {'theme': 'base',
         }
}%%
graph TD;

  subgraph dnaTrace
  A1(["get_numpy_arrays() | Load Numpy arrays to dictionary indexed by number"]) --> A2(["skimage.filters.gaussian() | Filter full image"])
  A2 -- For each image --> A3(["get_disordered_trace() | extracts mask"])
  A3 --> A4(["purge_obvious_crap() | Removes ites if len() < 10 (i.e. small objects) "])
  A4 --> A5(["linear_or_circular on unordered traces() | linear or circular molecule"])
  A5 --> A6(["get_ordered_traces() | Reorders points in the array?"])
  A6 --> A7(["linear_or_circular() on ordered traces"])
  A7 --> A8(["get_fitted_traces()"])
  A8 --> A9(["get_splined_traces()"])
  A9 --> A10(["measure_contour_length()"])
  A10 --> A11(["measure_end_to_end_distance()"])
  A11 --> A12(["report_basic_stats()"])
  end

  subgraph "get_disordered_trace()"
  A3 --> B1(["ndimage.binary_dilation() | extracts mask"])
  B1 --> B2(["scipy.ndimage.gaussian_filter molecule()"])
  B2 --> B3(["getSkeleton()"])
  B3 --> A4
  end

  subgraph "getSkeleton()"
  B3 --> C1(["Skeletonize | to be replaced by get_skeleton()"])
  C1 --> B3
  end

  style A1 fill:#648FFF,stroke:#000000
  style A2 fill:#648FFF,stroke:#000000
  style A3 fill:#648FFF,stroke:#000000
  style A4 fill:#648FFF,stroke:#000000
  style A5 fill:#648FFF,stroke:#000000
  style A6 fill:#648FFF,stroke:#000000
  style A7 fill:#648FFF,stroke:#000000
  style A8 fill:#648FFF,stroke:#000000
  style A9 fill:#648FFF,stroke:#000000
  style A10 fill:#648FFF,stroke:#000000
  style A11 fill:#648FFF,stroke:#000000
  style A12 fill:#648FFF,stroke:#000000
  style B1 fill:#DC267F,stroke:#000000
  style B2 fill:#DC267F,stroke:#000000
  style B3 fill:#DC267F,stroke:#000000
  style C1 fill:#FE6100,stroke:#000000