Free online NDPI to PNG converter

NDPI files are whole-slide microscopy images, while PNG is supported by ordinary image editors, browsers, and presentation software. Converting is useful when you need to share a slide image, annotate a selected region, or use microscopy data in software that cannot read Hamamatsu’s format.

What the NDPI format is

NDPI is Hamamatsu’s digital pathology format for scanned microscope slides produced by NanoZoomer systems. It commonly contains a very large, multi-resolution image pyramid, and may also store multiple focal planes, label images, and slide metadata.

You typically encounter NDPI files in pathology laboratories, medical research, university imaging facilities, and datasets exported from Hamamatsu NanoZoomer scanners. Because a slide can contain billions of pixels, an NDPI file is much larger and more complex than an ordinary photograph. Support varies between applications; QuPath, Fiji with Bio-Formats, and software based on OpenSlide can read many NDPI files.

What the PNG format is

PNG is a lossless raster image format supported by web browsers, image editors, office software, and most operating systems. It preserves exact pixel values during encoding and supports transparency, but it does not preserve NDPI’s slide pyramid, focal-plane data, annotations, or scanner metadata in a generally usable form.

PNG is suitable for figures, screenshots, annotated tissue regions, reports, and web display. It is usually unsuitable as a replacement archive for the original slide because a full-resolution whole-slide export can be extremely large.

How to actually convert NDPI to PNG

Using 101convert.com

1. Open the NDPI-to-PNG converter on 101convert.com; the service can be used free without installing software.
2. Upload the .ndpi file and select PNG as the output format.
3. Start the conversion and download the resulting .png file when processing finishes.

For very large slides, upload limits, processing time, and the output dimensions may prevent a complete full-resolution conversion. Exporting a selected region with desktop pathology software is usually more practical.

Using QuPath

1. Install QuPath and open the NDPI file with File → Open. QuPath uses Bio-Formats or OpenSlide support depending on the file and configuration.
2. Set the image view to the required magnification. For a complete slide, use the image export function; for a tissue section, define a rectangular region or annotation first.
3. Choose File → Export image or the corresponding export command in your QuPath version, select PNG, and set the output resolution or downsampling factor.
4. Export the image. If the selected area exceeds PNG or memory limits, export several tiles instead of one enormous file.

Using Fiji and Bio-Formats

1. Install Fiji, which includes the Bio-Formats importer.
2. Open the file with File → Open, or use Plugins → Bio-Formats → Bio-Formats Importer.
3. Choose the required series, resolution level, and region in the importer. Avoid opening the full native-resolution slide unless the computer has sufficient memory and storage.
4. Save the displayed or selected image with File → Save As → PNG.

Quality, compatibility, and limitations

PNG compression is lossless, but conversion cannot restore detail that was discarded by selecting a lower pyramid level or downsampling. Record the exported pixel size, magnification, and region coordinates if the PNG will be used for measurements or publication.

A full-slide PNG may exceed common image-dimension or memory limits. QuPath or Fiji can export a downsampled overview or separate tiles more reliably than a single native-resolution image. Keep the original NDPI file for diagnostic, quantitative, or archival use, because PNG normally omits the NDPI image pyramid, scanner metadata, focus layers, and pathology-specific structure.

NDPI files can contain patient or specimen information in metadata or filenames. Remove identifying information before sharing exported images, and verify the PNG at 100% zoom after conversion to check cropping, orientation, color, and the selected resolution.