TGN dataset

Published: 17 June 2024| Version 1 | DOI: 10.17632/8gpvhrrghk.1
Eldirdiri Fadol Ibrahim Ibrahim


Step-by-Step Approach Verify Dataset and Annotations: Double-check that your annotations.csv file contains valid entries with correct paths (image_path) and corresponding labels (label). Load and Inspect Data: Make sure that df_annotations is correctly loaded and contains data. Print or inspect df_annotations.head() to see the first few rows and verify its structure. Debug and Visualize: Implement error handling and debugging statements to pinpoint where the issue might arise. Ensure that image paths are correctly formed and that images can be loaded using matplotlib. Display the Visualization: Use matplotlib to display the images along with their labels, ensuring the plot dimensions are correctly set. To implement Mask R-CNN with annotated data, we'll need to follow several steps including preparing the data, configuring the Mask R-CNN model, training it on the annotated dataset, and then using it for inference. Here’s a structured approach to accomplish this: Step-by-Step Guide to Implement Mask R-CNN with Annotated Data 1. Prepare the Dataset First, ensure your annotated data is structured correctly. This typically involves: Annotations: Each image should have corresponding annotations specifying the regions of interest (ROIs) and their labels. Image Loading: Load images and annotations into a format suitable for training Mask R-CNN. 2. Install Required Libraries Ensure you have the necessary libraries installed: 3. Customize Mask R-CNN for Your Dataset You might need to customize the Mask R-CNN configuration (mrcnn/ for your specific dataset. This involves setting parameters such as: Number of classes (NUM_CLASSES) Image resizing parameters Backbone network (default is ResNet101) 4. Prepare Data Loaders Create data loaders to feed data into Mask R-CNN: Dataset Class: Implement a custom dataset class (mrcnn/ that loads images and annotations. Data Generator: Create a data generator that preprocesses images and annotations for training. 5. Configure and Train the Model Configure and train Mask R-CNN using your annotated dataset: Model Configuration: Set up the Mask R-CNN model (mrcnn/ with your customized configuration. Training: Train the model using the prepared data loaders and appropriate training parameters (mrcnn/ 6. Evaluate and Fine-Tune After initial training, evaluate the model's performance: Validation: Evaluate on a validation set to assess metrics such as mAP (mean Average Precision). Fine-Tuning: Fine-tune hyperparameters or adjust the model architecture based on validation results. 7. Inference Use the trained Mask R-CNN model for inference on new data: Detection and Segmentation: Apply the model to detect and segment objects in new images. Visualization: Visualize the results of the model's predictions.


Steps to reproduce

dataset might contain: Possible Contents of Ultrasound Dataset Metadata Image Information: Image ID or Name: Unique identifier or filename of each ultrasound image. Image Path: File path or URL to locate the ultrasound image file. Patient Information: Patient ID: Identifier for the patient who underwent the ultrasound examination. Age: Age of the patient at the time of the ultrasound examination. Sex: Gender of the patient (Male, Female, or other categorizations). Ultrasound Examination Details: Date and Time: Date and time when the ultrasound examination was performed. Ultrasound Type: Type of ultrasound examination (e.g., abdominal, thyroid, obstetric). Probe Type: Type of ultrasound probe used (e.g., linear, convex). Anatomical Information: Body Part: Area or organ of the body examined with ultrasound (e.g., liver, thyroid gland, fetus). Measurements: Quantitative measurements obtained from the ultrasound (e.g., size of a nodule, diameter of an organ). Diagnostic Information: Findings: Description of ultrasound findings or abnormalities observed (e.g., cyst, mass, nodules). Diagnosis: Preliminary or final diagnosis based on ultrasound findings. Clinical Information: Referring Physician: Name or identifier of the physician who referred the patient for ultrasound examination. Clinical History: Relevant medical history or symptoms prompting the ultrasound examination. Additional Annotations: Annotations: Additional notes or annotations related to the ultrasound images or findings. Quality Assessment: Quality assessment metrics or indicators for the ultrasound images. Example Scenario For instance, if the dataset pertains to thyroid ultrasound examinations, it might include metadata fields such as: Image ID: Unique identifier for each ultrasound image. Image Path: File path to locate the ultrasound image file. Patient ID: Identifier for the patient. Age: Age of the patient. Sex: Gender of the patient. Date and Time: Date and time of the ultrasound examination. Ultrasound Type: Type of ultrasound (e.g., thyroid). Probe Type: Type of ultrasound probe used. Body Part: Thyroid gland. Measurements: Size and characteristics of thyroid nodules. Findings: Description of nodules (e.g., cystic, solid). Diagnosis: Preliminary diagnosis (e.g., benign, malignant). Conclusion Understanding the specifics of ultrasound_dataset_metadata.csv involves examining its columns and possibly consulting documentation provided with the dataset. This description gives you a general idea of what to expect in such a dataset, which typically serves as crucial contextual information for ultrasound images used in medical diagnostics and research. Adjustments might be needed based on the exact structure and intended use of the dataset.


Endocrinology, Endocrine Oncology