Medical 2D images

Overview

Medical 2D Converter allows to import 2D files with .nrrd, .dcm, .nii and .nii.gz extensions. Files with extensions different from .nrrd will be converted to .nrrd

While this converter primarily supports 2D medical images, it is possible to import 3D files. However, please note that 3D files will be transposed and sliced along the axial plane. This process converts the 3D image into a series of 2D slices, which can then be viewed and analyzed individually.

Format description

Supported image formats: .nrrd, .dcm, .nii and .nii.gz With annotations: No Grouped by: Any structure (will be uploaded as a single dataset)

Input files structure

Example data: download ⬇️

Recommended directory structure:

  📦project name
  ┣ 📜Image_1.dcm
  ┣ 📜Image_2.dcm
  ┣ 📜Image_3.dcm
  ┣ 📜Image_4.dcm
  ┣ 📜Image_5.DCM
  ┣ 📜Image_6.nrrd
  ┗ 📜Image_7.nii

2D Medical Image Formats Explained

• DCM

  DCM file is an image following Digital Imaging and Communications in Medicine (DICOM) format. Format is used to store various medical images like CT scans, MRIs, PET, ultrasound, etc.

  Uses .dcm and .DICOM extensions

  If your DICOM data contains one of the following metadata fields, it will be used as group tag in the project:

  • StudyInstanceUID

  • StudyID

  • SeriesInstanceUID

  • TreatmentSessionUID

  • Manufacturer

  • ManufacturerModelName

  • Modality

  Moreover, all other DICOM metadata will be saved as image metadata and can be viewed in the Labeling interface.

• NRRD

  NRRD file is a medical imaging format. It is used to store 2D and 3D images along with metadata. It is commonly used in medical imaging.

  Uses .nrrd extension.

• NII

  NII format is commonly used to store magnetic resonance imaging (MRI) data.

  Uses .nii and .nii.gz extensions.

Medical data import results

Useful links

• [Supervisely Ecosystem] Import DICOM studies

• Nearly Raw Raster Data (NRRD): Format, Examples etc.

• Overview of The Content of The DICOM Standard

• Neuroimaging Informatics Technology Initiative (NIfTI)