Frequently Asked Questions (FAQ) about Proxan

What does it do?

Based on their colour, Proxan identifies two sets of objects on the image. The reference set is some inherent feature of the biological matrix, for example blood vessels or certain kind of cells. The other set, that Proxan calls the active set, is some biological phenomenon that is not part of the matrix, such as plaques of blood or a certain protein in cells or in the intercellular space. Proxan does not know what they are and she does not care, as long as they are marked with distinct colours. After extracting these objects from the image, Proxan tries to determine if there is a spatial relationship between the two sets. She achieves that by generating artificial images on which the active objects are randomly distributed.

On each artificial image the reference objects, that is, the biological matrix is unchanged. The number, shape and orientation of the active objects are also preserved. However, the locations of the active objects are randomised, adhering to certain rules.

Proxan then calculates the distances between reference and active objects for each image. These numbers form a statistics describing the distance distribution between the reference and active object sets on your image, assuming that there is no relationship between the two sets. Finally, Proxan compares the distances on your original image against the statistics that she has obtained from the random image set. From that she concludes whether on the original image there is a spatial correlation between the two object sets or not.

How much does it cost?

Proxan is free software, both monetarily and in terms of your rights.
Please note that despite being free, Proxan is not in the public domain. Bendor Research owns the copyright for it, and it is licenced to you under the terms of the Free Software Foundation's GNU General Public License (GPL). That license grants you the right to use, re-distribute and modify Proxan. It also allows you to use bits of Proxan in other programs you might write, on the condition that when you release those programs, or a modified version of Proxan, you release them under the GNU General Public License.
Furthermore, the GPL restricts our powers over Proxan's fate: even though we are the copyright holders, we can not revoke the above mentioned rights from you and under no circumstances can we demand you to cease to use, distribute or modify Proxan.
At the same time the GPL requires you to waive your rights to demand any guarantee, warranty or liability from us with regards to Proxan; if you use it, you use it at your own risk and you are solely responsible for any and all consequences of your using it.

Proxan does not do what I want. How can I sue you?

You can not. Proxan's license clearly states that Proxan comes with no warranty whatsoever. We do not guarantee that it works, that it does what we tell you it does or that it causes no harm to you or a third party. We assume no responsibility and accept no liability for any of the above or anything else with relation to Proxan. You use it at your own risk. By using it you accept all liabilities arising out of its use. If Proxan blows up your computer, makes you a laughing stock, causes world famine or wipes out the peaceful folk of the 6th planet of Theta Draconis because of your using it, that is all your responsibility.
If you think that the above is arrogant and harsh, please read very carefully the End User License Agreement (EULA) of any Microsoft^® product you might own. Alternatively, read the license agreement of more or less any commercial software product you have. You will be surprised.

What do I need to run Proxan?

First of all, you need a GNU/Linux (Linux for short) system. If you don't know what it is, you might take a look at this site. You will also need gcc and gmake from the GNU Project, these come with your Linux distribution. Proxan uses the GTK+ library as well as libtiff, the TIFF image library. As far as we know, all current Linux distributions contain these. However, if yours does not, you can get the GTK+ from here and the TIFF library from here.

Proxan needs lots of memory and a fast processor. She runs comfortably on a modern machine but as a minimum, you should have a Pentium-III running at at least 600MHz and your machine should have a minimum of 128MB of RAM. Given enough swap space she would run on a lesser machine but you will get frustrated of waiting for her.

Proxan does not run on Microsoft^® Windows^® systems.

Does it run only on Linux?

The GTK+ and the TIFF library are available for pretty much any unix-ish system. Proxan uses only basic system functions, it has nothing inherently Linux-specific in it. Therefore, compiling Proxan on Solaris, *BSD or any other unix-type system should be a matter of possibly editing the library and include path statements in the Makefile, if that. Of course, you need GTK+ and libtiff installed, as well as gcc and GNU make.

Will you port Proxan to the Mac?

We do not have a Mac and since we do not need it for our everyday operations, it would be hard to justify buying one just to port Proxan. By our best knowledge GTK+ has been ported to MacOS-X. In the heart of MacOS-X there is a unix variant, so the rest of Proxan would run comfortably there. It would probably be easy to find someone with both Mac and Linux experience and access to port it. We'd be glad to host the Mac version on our website.

Will you port Proxan to Microsoft^® Windows^®?

No. However, if you find someone who does, we would host that version as well.

Will you develop Proxan further?

Yes, we will. We have a handful of new features in mind that we want to add and of course we will fix all pending issues with the existing version. Keep in mind, however, that Proxan is not our main activity, she is being written when we can afford the time and resources needed for her development. Nevertheless, we will not abandon her.

Why do you sometimes use the pronoun 'she' when referring to Proxan?

The name Proxan comes from proximity analysis. It sounds similar to the female name Roxan. While you are developing a program, you sometimes start to think of it as a being rather than just an algorithm. That happened with Proxan and during the development process 'it' slowly became a 'she'. Naturally, we can not licence her, so for that purpose Proxan is an 'it'. Otherwise, a 'she'. Especially when she is moody... :-)