Tools

Overview

Two command line utilities ship with every SlideIO package:

• slideio-converter converts a slide, or a region of one, into a tiled pyramidal SVS or OME-TIFF file.
• slideio-tiffinspector prints the directory structure of a TIFF file, which is how you find out what a pyramidal TIFF actually contains.

Neither needs Python, and neither needs the library to be built: they are part of the binary distributions.

Installation

The tools are in every package on the Downloads page.

Debian and Ubuntu

They are a separate package, so that installing the library does not put unversioned programs in /usr/bin:

sudo apt install ./slideio-tools_<version>_amd64.deb

That puts both on your PATH.

macOS and Windows

Unpack the archive. The tools are in its bin directory and run from there — they carry an RPATH into the package’s lib, so nothing has to be set up first. On Windows, add bin to PATH if you want to run them from anywhere:

set PATH=C:\slideio\bin;%PATH%

A note if you build from source: in the build tree the executables are called converter and tiffinspector. The distributions rename them at install time, because converter is too generic a name to put in a shared bin directory.

slideio-converter

Converts a slide to a tiled, pyramidal image. The output carries a zoom pyramid, so the result stays usable at any magnification rather than being a single enormous plane.

slideio-converter <input> <output> [options]

Both paths are required. By default the output is an OME-TIFF with JPEG 2000 compression, 512-pixel tiles, and a pyramid whose depth is chosen from the image size.

Options

--help lists them all, with the library version in the header.

Examples

Convert a slide to OME-TIFF with the defaults:

slideio-converter image.czi image.ome.tiff

Produce an SVS with JPEG compression at quality 90:

slideio-converter image.ndpi image.svs -f SVS -m Jpeg -q 90

Convert one region of the second scene:

slideio-converter image.czi region.ome.tiff -n 1 -r 10000,8000,4096,4096

Check what a conversion would produce without doing it:

slideio-converter image.vsi out.ome.tiff --info-only

Reading and encoding run on separate thread pools, and reads of one scene run in parallel on most formats, so a conversion uses the machine it is given. Cap either pool with --reading-threads or --encoding-threads when converting several files at once.

slideio-tiffinspector

Prints every TIFF directory in a file, one after another:

slideio-tiffinspector <input>

It takes exactly one argument and writes to standard output, so it pipes and redirects like any other filter.

For each directory it reports the geometry and encoding — width and height, whether the directory is tiled and with what tile size, channels, bits per sample, photometric interpretation, compression, data type, rows per strip, strip size, interleaving, subfile type — along with the directory index, its offset in the file, the description, resolution, position, and the software and dateTime tags. Where the file carries an ICC colour profile, the profile is summarised too: its size, version, data and connection spaces, rendering intent, manufacturer, model and white point.

This is the tool for answering questions that the image itself does not: how many pyramid levels a slide really has and at what sizes, whether levels are tiled or stripped, what compression each one uses, which directory holds the thumbnail or label, and whether a slide carries a colour profile at all.

slideio-tiffinspector slide.svs | head -40
slideio-tiffinspector slide.svs > structure.txt

It works on any TIFF, including the formats SlideIO reads that are TIFF underneath — SVS, Philips TIFF, NDPI, QPTIFF and OME-TIFF — and on output written by slideio-converter, which makes it the quickest way to confirm a conversion produced the pyramid you expected.