DICOM Tag Layouts
Follow the end to end walkthrough below to learn how to set up a custom Label Editor configuration based on DICOM tags. This End-to-end example assumes you configure the Label Editor so that two files are displayed at a given time.
This end-to-end example assumes that your files are stored in cloud storage.
STEP 1: Create JSON File for Data Registration
Before registering your cloud data to Encord you must first create a JSON file specifying the files you want to register. The following JSON file registers 3 DICOM series consisting of 4 files each.
STEP 2: Register files with Encord
Create a Folder to Store Your Files
All files in Encord must be stored within folders. Therefore, you need to create a folder before registering any data with Encord. To create a folder:
- Navigate to Files under the Index heading in the Encord platform.
- Click the + New folder button to create a new folder. A dialog to create a new folder appears.
-
Give the folder a meaningful name and description.
-
Click Create to create the folder. The folder is listed in Files.
Register Your Files
You can register your DICOM data using the JSON file you created, using the UI or the SDK.
Register data in the UI
Register data in the UI
- Navigate to Files section of Index in the Encord platform.
- Click into a Folder.
- Click + Upload files. A dialog appears.
- Click Import from cloud data.
Register data using in the SDK
Register data using in the SDK
To use your data in Encord, it must be uploaded to the Encord Files storage. Once uploaded, your data can be reused across multiple Projects and contain no labels or annotations themselves. Files stores your data, while Projects store your labels. The following script creates a folder in Files and uses your AWS integration to register data in that folder.
The following script creates a new folder in Files and initiates uploads from AWS. It works for all file types.
Upload is still in progress, try again later!
is returned, use the
script to check the upload status to see whether the upload has finished.Ensure that you:
- Replace
<private_key_path>
with the path to your private key. - Replace
<integration_title>
with the title of the integration you want to use. - Replace
<folder_name>
with the folder name. The scripts assume that the specified folder name is unique. - Replace
path/to/json/file.json
with the path to a JSON file specifying which cloud storage files should be uploaded. - Replace
A folder to store my files
with a meaningful description for your folder. - Replace
"my": "folder_metadata"
with any metadata you want to add to the folder.
The script has several possible outputs:
- “Upload is still in progress, try again later!”: The registration has not finished. Run this script again later to check if the data registration has finished.
- “Upload completed”: The registration completed. If any files failed to upload, the URLs are listed.
- “Upload failed”: The entire registration failed, and not just individual files. Ensure your JSON file is formatted correctly.
STEP 3: Set up Your Project
Create a Dataset
Create an Ontology
Create a Project
STEP 4: Create Custom Editor Layout
After creating your Project, import a custom layout for the Label Editor. Start by creating a JSON file that determines the layout.
Create a JSON for the Layout
Common layouts mammography files are a 2x2 grid, and 4x1 showing all files in a horizontal row.
- 2x2 layout: https://raw.githubusercontent.com/encord-team/Annotate/refs/heads/main/editor-layouts/examples/mammo2x2.json
- 4x1 layout: https://raw.githubusercontent.com/encord-team/Annotate/refs/heads/main/editor-layouts/examples/mammo4x1.json
Import the custom layout
- Navigate to the Project settings.
- Click on Editor Layouts.
- Click Upload JSON.
- Select the JSON file containing the layout you want the Label Editor to have.
What do the Layouts Look Like?
2x2 Mammography Layout:
4x1 Mammography Layout: