Convert TIFF to JPG or PNG

Converting 16-bit TIFFs without losing the picture

PNG and JPEG as used on the web hold 8 bits per channel, so a 16-bit microscope image has to be mapped onto 256 levels. A converter that maps the full 0–65,535 range makes a typical camera image, which uses a few thousand levels, nearly black. Here each channel's range starts at its 0.1st–99.9th percentile (Auto contrast); type a minimum and maximum to apply the same mapping to several images so they stay comparable, or choose Full range. Keep the original TIFF for measurements: an 8-bit export changes intensities, and PNG and JPEG do not carry the pixel size.

What you can export

• One plane or all of them: pages, Z planes and time points, each saved as its own file.
• Composite or separate channels: a coloured overlay of the channels you leave on, or each channel as its own grayscale image.
• Whole-slide images: pick a pyramid level up to 16,384 pixels a side (browsers cannot hold larger images). For a full-resolution export, convert to OME-TIFF on the desktop instead (how).
• PNG is lossless; JPEG is smaller, with the quality you set.

The same conversion in Fiji or on the command line

Fiji: Image › Adjust › Brightness/Contrast, Apply, then Image › Type › 8-bit (or RGB Color for composites) and File › Save As › PNG. ImageMagick: magick input.tif -auto-level -depth 8 output.png (add [0] after the input name for the first page only). Python: read with tifffile.imread, rescale to 0–255 with numpy, write with imageio.

What it does not open

• JPEG 2000 SVS (Aperio compression 33003/33005), JPEG XR and JPEG XL cannot be decoded in a browser without WebAssembly, which this page does not load.
• Not TIFF-based: CZI, ND2, LIF, MRXS, VSI, IMS, OIB/OIR and DICOM need a desktop reader. NDPI is TIFF-like but stores each level as one huge JPEG, too large for a browser tab.
• OME-TIFF with several series shows the first series.
• No measurements, annotations or analysis: it is a viewer.

For those formats, and for measuring, annotating and counting cells on your own images, SlideScope opens 34 microscope and slide-scanner formats on Windows and Mac. SlideScope, the desktop microscopy app made by the same team, is a paid app with a free sample library (every tool) and a 3-day free trial for your own images. Free alternatives: Fiji (Bio-Formats) and QuPath.

How it opens a file without uploading it

When you choose a file, the browser hands this page a handle to it on your disk. The page reads only the bytes it needs: the TIFF directory first, then the tiles for the part of the image on screen, and decodes them in the page with an open-source TIFF reader (geotiff). Nothing is sent to a server, so unpublished data and slides with patient labels stay on your computer, and multi-gigabyte slides open in seconds because they are never copied anywhere. Close the tab and the file is gone from the page.

The page loads its own scripts from slidescope.science and the site's privacy-respecting page-view counter; neither ever sees your image. Open-source licences: image-tools-vendor.LICENSE.txt.

Questions