OCT QA

This gear assesses the quality of OCT volumes and their slices. The criteria to flag a slice is being bigger than 1.5 * Interquartile Range (IQR) or smaller than 1.5 * IQR for each of the four measurement tests. If any slices are flagged in any of the four tests, the overall_qc test will be set to fail. All test results are saved in the input file's info dictionary under "qc":"oct-qa".

1. dynamic_range: Dynamic range of the retinal image slice.
2. variance_extraretinal: the variance of the extraretinal/vitreous region. This region gets segmented based on Otsu's thresholding method; it provides an estimate of the base noise of the image.
3. variance_intraretinal: the variance of the retinal region. This is similarly derived as extraretinal variance.
4. sharpness_slope: the sharpness of the edges between the black regions of the vitreous and the bright regions of the retinal layers; a higher slope indicates a sharper image.

The gear will:

• Update the metadata of the input file. See example output below.
• Generate histograms for three indexes so that low-quality slices can be flagged; these histograms will only be generated if save_figures_if_fail is true.
• Output a csv with slice QA measurements/indexes for further analysis.

"qc": {
  "oct-qa": {
    "job_info": {
      "version": "0.0.5-d",
      "job_id": "",
      "inputs": {
        "raw_input": {
          "parent": {
            "id": "60f71983a7fe04f03224792e",
            "type": "acquisition"
          },
          "file_id": "610d9bff9c47094a376b8ddb",
          "version": 1,
          "file_name": "oct_volume_test.npy"
        }
      },
      "config": {
        "debug": true,
        "save_figures_if_fail": true
      }
    },
    "dynamic_range": {
      "state": "PASS",
      "data": {
        "Mean Dynamic range": 1.044,
        "Standard deviation Dynamic range": 0.021,
        "Outliers Dynamic range": "No slices flagged"
      }
    },
    "variance_extraretinal": {
      "state": "PASS",
      "data": {
        "Mean Variance Extraretinal region": 255.445,
        "Standard deviation Variance Extraretinal region": 14.182,
        "Outliers Variance Extraretinal": "No slices flagged"
      }
    },
    "variance_intraretinal": {
      "state": "PASS",
      "data": {
        "Mean Variance Intraretinal": 2050.806,
        "Standard deviation Variance Intraretinal": 134.474,
        "Outliers Variance Intraretinal": "No slices flagged"
      }
    },
    "sharpness_slope": {
      "state": "PASS",
      "data": {
        "Mean Sharpness slope": 19.047,
        "Standard deviation Sharpness slope": 0.487,
        "Outliers Sharpness slope": "No slices flagged"
      }
    },
    "overall_qc": {
      "state": "PASS",
      "data": {
        "result": "all qc tests passed"
      }
    }
  }
}

Usage

Inputs

• raw_input: Raw OCT slices (.npy, .dcm or .dcm.zip)

Configuration

• debug (boolean, default False): Include debug statements in output.
• save_figures_if_fail (boolean, default False): If any of the qa tests fail, save all generated histograms within the parent container.

Contributing

For more information about how to get started contributing to that gear, checkout CONTRIBUTING.md.