Free online NDPI to JPG converter

What the NDPI format is

NDPI is a proprietary whole-slide image format created mainly by Hamamatsu NanoZoomer scanners. It can contain extremely large, multiresolution microscope images used in digital pathology, research, and slide archiving.

You may encounter NDPI files in Hamamatsu NDP.view2 software, QuPath, Fiji/ImageJ with Bio-Formats, and applications built on the OpenSlide library. An NDPI file can be many gigabytes and may include several resolution levels, so it is not equivalent to an ordinary single-layer photograph.

What the JPG format is

JPG, also called JPEG, is a widely supported raster image format using lossy compression. It is suitable for slide previews, reports, presentations, websites, email attachments, and general image editing.

JPG files are normally much smaller than NDPI files and open without specialist microscopy software. The format does not preserve the NDPI pyramid, scanner-specific metadata, annotations, multiple focal planes, or diagnostic image data.

How to actually convert NDPI to JPG

Use the online converter

You can convert the file on 101convert.com for free without installing software. Upload the .ndpi file, choose JPG as the output format, start the conversion, and download the resulting image. For very large slides, use a desktop method or export a smaller region because a full-resolution JPG may exceed memory or file-size limits.

Export a slide preview with OpenSlide and Python

OpenSlide is designed to read whole-slide formats, including many NDPI files. Install the OpenSlide system library for your operating system, then install the Python bindings and Pillow:

pip install openslide-python pillow

Save this as ndpi_to_jpg.py and replace the input filename:

import openslide

slide = openslide.OpenSlide("sample.ndpi")
image = slide.get_thumbnail((6000, 6000)).convert("RGB")
image.save("sample.jpg", "JPEG", quality=90, optimize=True)

Run it with:

python ndpi_to_jpg.py

get_thumbnail() creates a complete-slide preview constrained to 6000 by 6000 pixels. Increase those dimensions for more detail, but check available memory before exporting very large images.

Export a selected high-resolution region

For a tissue area that must retain more detail, read a region at a chosen pyramid level instead of converting the entire slide:

import openslide

slide = openslide.OpenSlide("sample.ndpi")
region = slide.read_region((10000, 15000), 0, (4000, 3000)).convert("RGB")
region.save("region.jpg", "JPEG", quality=95)

The coordinates are measured from the top-left corner at level 0, usually the highest available resolution. Change the location and dimensions to match the required tissue area. Level 0 coordinates and available levels can be inspected with slide.level_dimensions.

Use QuPath or Fiji

QuPath can open supported NDPI files through OpenSlide. Open the slide, select the required view or region, and use File → Export images to export a JPG. In Fiji/ImageJ, open the file through File → Open Samples or the Bio-Formats importer, then use File → Save As → JPEG. Menu names can vary by application version and installed plugins.

Quality, compatibility, and limitations

JPG export is lossy. Use a quality value around 90–95 for general use and avoid repeatedly opening and resaving the same JPG. PNG or TIFF is preferable when pixel-level analysis, annotations, or lossless preservation is required.

A full-slide JPG may still be too large for some viewers even after compression. Exporting a thumbnail or region is generally more compatible than flattening the entire slide into one maximum-resolution image.

Do not use a JPG as the archival or diagnostic replacement for the NDPI source. It discards the multiresolution structure and may introduce compression artifacts that affect fine cellular detail. Keep the original NDPI and treat the JPG as a presentation or sharing copy.