Request some help on getting started with OpenSlide

Thu Feb 18 05:38:25 EST 2016

Hi Benjamin,

Sorry, I guess I could have mentioned that too :)

I followed the instructions on the READ_ME.txt file

How to build?
> =============
> ./configure
> make
> make install
> (If building from the Git repository, you will first need to install
> autoconf, automake, libtool, and pkg-config and run "autoreconf -i".)

So after ensuring the packages are installed and after running "autoreconf
-i", I run ./configure. The terminal output gives me the following error
(see the config.log for more details):

checking for CAIRO... yes
> checking for LIBPNG... yes
> checking for GDKPIXBUF... yes
> checking for LIBXML2... no

*configure: error: Package requirements (libxml-2.0) were not met:*

> No package 'libxml-2.0' found
>

Consider adjusting the PKG_CONFIG_PATH environment variable if you
> installed software in a non-standard prefix.
>

Alternatively, you may set the environment variables LIBXML2_CFLAGS
> and LIBXML2_LIBS to avoid the need to call pkg-config.
> See the pkg-config man page for more details.

I went on to try and install the package and found that it was "libxml2"
and not "libxml-2.0". After installing, the ./configure gives the same
errors. I am thus unable to run make and make install.

Hope you can help me get started? Thanks for the helping so far, it is
appreciated!

Kind regards,
Evert

On Thu, Feb 18, 2016 at 5:07 AM, Benjamin Gilbert <bgilbert at cs.cmu.edu>
wrote:

> On Wed, Feb 17, 2016 at 11:21:05AM +0200, Evert Trollip via
> openslide-users wrote:
> > It seems that it doesn't seem to find the library file functions even
> > though I added the header file and linked against openslide? Any help
> would
> > be appreciated.
>
> Hi Evert,
>
> You mentioned extracting the OpenSlide sources, but didn't say anything
> about building them.  :-)  Were you able to build and install OpenSlide?
> If so, you might want to check that the ${libdir} in your project is set to
> the directory containing the installed OpenSlide .so file.
>
> --Benjamin Gilbert
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20160218/f6b97856/attachment-0001.html>
-------------- next part --------------
OpenSlide

Carnegie Mellon University and others

http://openslide.org/

==========================

What is this?
=============

This library reads whole slide image files (also known as virtual slides).
It provides a consistent and simple API for reading files from multiple
vendors.

What is the license?
====================

This code is licensed under the GNU LGPL version 2.1, not any later version.
See the file lgpl-2.1.txt for the text of the license.

Requirements
============

This library requires zlib, libpng, libjpeg, libtiff, OpenJPEG 1.x or >= 2.1,
GDK-PixBuf, libxml2, SQLite >= 3.6.20, cairo >= 1.2, and glib >= 2.16.
Leica and Ventana support require libtiff >= 4.

If you want to run the test suite, you will need PyYAML, python-requests,
xdelta3, cjpeg and djpeg (from libjpeg), a Git checkout of OpenSlide,
at least one installed font, and > 120 GB of disk space.  Valgrind mode
requires Valgrind, plus debug symbols for library dependencies (particularly
glib2) and Fontconfig.  Profile mode requires Valgrind.  Coverage mode
requires gcov and Doxygen.

Features
========

The library can read Aperio, Hamamatsu, Leica, MIRAX, Sakura, Trestle,
and Ventana formats, as well as TIFF files that conform to a simple
convention. (InterScope files tend to be readable as this generic TIFF.)

More information about formats is here:
http://openslide.org/formats/

An openslide_t object can be used concurrently from multiple threads
without locking. (But you must lock or otherwise use memory barriers
when passing the object between threads.)

Properties
==========

The library exposes certain properties as string key-value pairs for
a given virtual slide. (These are accessed by way of the
"openslide_get_property_names" and "openslide_get_property_value" calls.)

These properties are generally uninterpreted data gathered from the
on-disk files. New properties can be added over time in subsequent releases
of OpenSlide. A list of some properties can be found at:
http://openslide.org/properties/

OpenSlide itself creates these properties (for now):

 openslide.background-color
   The background color of the slide, given as an RGB hex triplet.
   This property is not always present.

 openslide.bounds-height
   The height of the rectangle bounding the non-empty region of the slide.
   This property is not always present.

 openslide.bounds-width
   The width of the rectangle bounding the non-empty region of the slide.
   This property is not always present.

 openslide.bounds-x
   The X coordinate of the rectangle bounding the non-empty region of the
   slide. This property is not always present.

 openslide.bounds-y
   The Y coordinate of the rectangle bounding the non-empty region of the
   slide. This property is not always present.

 openslide.comment
   A free-form text comment.

 openslide.mpp-x
   Microns per pixel in the X dimension of level 0. May not be present or
   accurate.

 openslide.mpp-y
   Microns per pixel in the Y dimension of level 0. May not be present or
   accurate.

 openslide.objective-power
   Magnification power of the objective. Often inaccurate; sometimes missing.

 openslide.quickhash-1
   A non-cryptographic hash of a subset of the slide data. It can be used
   to uniquely identify a particular virtual slide, but cannot be used
   to detect file corruption or modification.

 openslide.vendor
   The name of the vendor backend.

Other Documentation
===================

The definitive API reference is in openslide.h. For an HTML version, see
doc/html/openslide_8h.html in this distribution.

Additional documentation is available from the OpenSlide website:
http://openslide.org/

The design and implementation of the library are described in a published
technical note:

 OpenSlide: A Vendor-Neutral Software Foundation for Digital Pathology
 Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, M. Satyanarayanan
 Journal of Pathology Informatics 2013, 4:27

 http://download.openslide.org/docs/JPatholInform_2013_4_1_27_119005.pdf

There is also an older technical report:

 CMU-CS-08-136
 A Vendor-Neutral Library and Viewer for Whole-Slide Images
 Adam Goode, M. Satyanarayanan

 http://reports-archive.adm.cs.cmu.edu/anon/2008/abstracts/08-136.html
 http://reports-archive.adm.cs.cmu.edu/anon/2008/CMU-CS-08-136.pdf

Acknowledgements
================

OpenSlide has been supported by the National Institutes of Health and
the Clinical and Translational Science Institute at the University of
Pittsburgh.

How to build?
=============

./configure
make
make install

(If building from the Git repository, you will first need to install
autoconf, automake, libtool, and pkg-config and run "autoreconf -i".)

Good luck!
-------------- next part --------------
A non-text attachment was scrubbed...
Name: config.log
Type: text/x-log
Size: 40120 bytes
Desc: not available
URL: <http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20160218/f6b97856/attachment-0001.bin>