Scientific Image DataBase
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Welcome to the

Scientific Image DataBase (SIDB)

Hosted at Sourceforge

Version 0.41 was released July 10, 2006.

Improved 3D thumbnails with multiple projections. Improved upload notifications. Some bugs solved.


SIDB is a web-driven database for images. Started as a project by and for undergraduate computer sciences students from the University of Utrecht, it matured at the Institute for Molecular Plant Sciences from the University of Leiden, the Netherlands, where SIDB is now used by many to archive images and other file types. Currently SIDB keeps being developed under the EU 3D-genome project and the AUTOMATION project, becoming also a programmable restoration and analysis on-line tool.

What it does

SIDB archives 2-D, 3-D images, time series or any kind of file. Image files are stored unchanged in a central directory (archive). Users of the system are subdivided in groups, and whoever owns an image (by uploading it) can determine who else on the system is allowed to view and use the image. Files can be uploaded through HTML, or using a mounted (smb, NFS, etc..) drive. Entering meta-data is facilitated by user-definable templates. The meta-data fields currently in use have been designed for images obtained by (fluorescence) microscopy. When combined with cheap, large hard drives and a fail-save backup mechanism, SIDB provides a perfect means to archive images within the setting of small to medium-sized research groups. However, it might be of use wherever people collaborate on images.

How it works

SIDB consists of PHP scripts communicating with a postgresQL database. It uses ImageMagick's convert to generate thumbnails from 2-D images, and a freeware Huygens Scripting to generate thumbnails from 3-D images. MPEG movies from 3-D images are made by Huygens, convert, and mpeg2encode. The system has been tested on linux (suse 7.0/7.1 and redhat 7.0/7.1), Mac OS X (10.1) and SGI Irix (6.5) but should work (or relatively easily be made workable) wherever Apache, php, postgresql and Imagemagick function. Once these components are up and working, installation of SIDB is simple due to a html installation form.

As all the database intelligence is on the server side, that serves plain HTML pages and forms, any kind of HTML browser can be used to access the SIDB. It is completely browser independent, and has been tested even with very simple ones on mobile devices.


To get a better idea what SIDB is about visit a working installation. Login as guest, password guest.


The Code

Please send bug reports and comments to Jose Viña, or use the sourceforge site. Last updated July 10, 2006.

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SVI Group University of Utrecht