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bbc2digital's Introduction

bbc2digital

Tools and processes to convert the Bolton-Brush Collection to digital format.

Background

The Bolton Brush Growth Study Collection encompasses various types of X-rays, including lateral and poster-anterior X-rays of the cranium, as well as X-rays of the hands, wrists, elbows, knees, chest, pelvis, foot, and ankle, gathered from over 4000 subjects. This comprehensive collection also consists of dental cast models and paper charts, serving as a valuable resource for studying human growth and development. The majority of X-rays were collected in the 1930s, but the collection extended until the 1980s. To safeguard these valuable assets, approximately 500,000 X-ray films have been scanned and digitized over time.

Due to the vast scale of this project, numerous researchers, volunteers, and workers have participated. Consequently, the resulting x-rays were often saved in manually generated folders, leading to many inconsistencies in formatting and organization. The aim of this project is to provide tools for:

  1. Cleaning up the existing, scanned data: This includes orienting all images consistently, dividing images that were collected on the same film, and saving them in a format intended for medical images (DICOM).
  2. Ensuring that the clean-up will be maintained in the future with new scans, preserving the integrity and usability of the collection.

Methods

We have chosen to use a neural network for correctly categorizing the images, determining their correct orientation, and identifying if and how to split them. A detailed explanation of the algorithms used can be found in the documentation/ folder within this repository.

The tools will also likely include a GUI for the operator, assisting them in adding new scans consistently and avoiding the reintroduction of inconsistencies that were previously cleaned up.

Future Uses

Other collections, such as the ones in the AAOF Legacy Collection, may also benefit from these tools. If needed, they can utilize them to achieve an organization based on an open standard like DICOM. This uniform approach could greatly enhance the research community's access to consistent and standardized datasets.

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bbc2digital's Issues

Step 4 Rotation

This step is necessary as some images have been stored rotated one way, others in another. Rotation is either 90, 180 or 270.
This task can be considered done when a tool has been developed which takes the following input and produces the following output.

INPUT: A classified BBC TIFF image with known class
OUTPUT: The correctly rotated image.

Step 3 Flip

This task is necessary because some radiographs have been placed in the scanner backwards, or images have been manually flipped by the operator.

This task can be considered done when a tool has been developed which:

INPUT: A classified BBC TIFF image
OUTPUT: A properly flipped (vertical/horizontal) TIFF BBC image.

Step 2: Classification

Tool necessary to make sure that the images in the BBC are in the proper folder. Since they were put there by humans, and stored in file system, it is very likely that some of them have been misplaced. This will cause a poor prediction capability of the model in the next step.

Task can be marked done when we have a tool:

INPUT: BBC TIFF radiograph (one of Lateral, Frontal, Pelvis, ...)
OUTPUT: Class of Radiograph (Lateral, Frontal, Pelvis, ...)

Develop Labelling Guidelines

Tool for Step 3 and Step 4. Process needed to clean up training data set.

This task can be considered done when we have found or developed a tool that can help the operators in the segmentation process. For example:

  1. Open tool
  2. Tool show first image
  3. Operator interacts by rotating and flipping the image
  4. Operator saves image
  5. Tool presents next image

The deliverable can be a tool or a procedure documented in a text file (for example .md).

Evaluation of splitting algorithms

Evaluation of feasibility of classic image processing techniques for automatic splitting of TIFF scans.
The deliverable for this issue is a jupyter notebook testing the following classic algorithms for automatic splitting:

  • Hough lines detection
  • ...

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