HPA Image Downloader

Requirements

• Windows computer
• Internet connection
• ImageDownloaderHPA.exe stored in an accessible folder

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Output location

Everything is saved under your user Downloads folder, inside HPA Images.

How to get the correct URL

1. Open Human Protein Atlas in your browser.
2. Navigate to the target gene/cancer page.
3. Make sure you are on the cancer tab where the image thumbnails are visible.
4. Copy the full URL from the address bar.

Tip: If the tool says it cannot find antibody IDs, the URL is usually not pointing to the correct thumbnail section.

Run the executable

1. Double click ImageDownloaderHPA.exe.
2. Paste the URL in the console (right click → paste or Ctrl+V).
3. Press Enter, then select 1 for .jpg or 2 for .tif.
4. Wait until it finishes; it will report the output folder and ask you to press Enter to exit.

Folder structure

Downloads → HPA Images → <GENE> → <ANTIBODY_ID> → <CancerSubtype>

• Images renamed as ID_<PatientID>_<n>.jpg/.tif
• One CSV per cancer subtype folder
• One “global” CSV at antibody root
• One “global” CSV at gene root (all antibodies)

CSV fields (high level)

Each row corresponds to one image and includes (among others):

• Gene, AntibodyID, CancerFolder
• ImageName, ImageLink
• PatientID, Gender, Age
• CancerType, CancerCode
• LocationCodes (tissue codes)

Resolution + format note

Image resolution is 0.5 μm/pixel (same for JPG and TIFF). JPG files are compressed (smaller size), but compression can slightly affect intensities.

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Common errors

• No antibody IDs found: verify the URL points to the cancer/IHC thumbnail section.
• No new folders in Downloads: check internet connection and URL correctness, and whether HPA Images already exists.