The Digital Communications in Medicine (DICOM) format is used to store CT scans, X-rays, and MRIs, as well as other medical images.

The Digital Communications in Medicine (DICOM) format is used to store CT scans, X-rays, and MRIs, as well as other medical images.

DICOM files may also contain patient identifying information, allowing the image to be connected to a specific individual. It is the most widely used medical imaging format in hospitals. DICOM maintains the high quality of the medical images. The patient information such as patient_id, abnormality, age, name, etc. can be recorded alongside the image in DICOM format.

Pydicom is a python library for working with dicom images. In this blog, we will install and utilize the common functions of pydicom library. You can also check the official documents of pydicom from this link.

There are multiple ways to install pydicom library in your environment. We preferred the following two ways; by using PIP or Conda.

How to install Pydicom using PIP or Conda

Install pydicom using PIP

pip install pydicom

Install pydicom using Conda

conda install -c conda-forge pydicom

After successful installation, you have to import the required libraries.

import pydicom
import matplotlib.pyplot as plt

The Pydicom library will be used to extract data from the Dicom file, while Matplotlib will be used to plot or display the Dicom file in pixels.

How to read DICOM image using Pydicom

dicom_path = "mammogram_1.dcm"
dicom_img = pydicom.dcmread(dicom_path)

The ‘pydicom.dcmread‘ read the Dicom file. In the above code, we read a Dicom file of a mammogram and store all the data into a ‘dicom_img’ variable.

How to get information from DICOM image

patient_id = dicom_img.PatientID
image_label = dicom_img.SeriesDescription

If you want to check out all the information stored inside the Dicom image. Simply print(‘dicom_img’), it will show the information of Dicom which you can use further for your tasks. For example; I just extract the patient ID and Series Description inside the Dicom file.

How to show DICOM image using Matplotlib

dicom_pixels = dicom_img.pixel_array
plt.imshow(dicom_pixels, cmap="gray")
plt.show()

Finally, if you want to show the Dicom image. You have to convert the Dicom into a pixels array. The ‘dicom_img.pixel_array‘ will perform this task and you can show it using matplotlib or any other library.

Complete Code

# Libraries

import pydicom
import matplotlib.pyplot as plt

# Read Dicom

dicom_path = "mammogram_1.dcm"
dicom_img = pydicom.dcmread(dicom_img)

# Get Dicom Information

patient_id = dicom_img.PatientID
image_label = dicom_img.SeriesDescription

# Convert Dicom into Image

dicom_pixels = dicom_img.pixel_array
plt.imshow(dicom_pixels, cmap="gray")
plt.show()