Frequently Asked Questions

Frequently Asked Questions


Frequently Asked Questions


Contact email: reyes {at} city [dot] ac [dot] uk


1) How does CAIMAN work?

2) What algorithms are being used?

3) Are the results always the same?

4) Does the type of image impact on the results?

5) Is it possible to add more algorithms?

6) Are there any test images?

7) How long does it take to process an image?

8) Are there any disclaimers?




1) How does CAIMAN work?

Caiman is an interactive image processing website that does not require any specific software, expertise or technical knowledge from the user other than knowing what kind of processing is required for an image.

CAIMAN combines four technologies:
  • the HTML-embedded scripting language PHP
  • a series of image processing algorithms that have been specifically designed to analyse different problems related to Cancer Research and Life Sciences
  • the powerful high-level technical computing language MATLAB,
  • the Interactive Object Management Environment (IOME) which is a unique, multi-purpose tool-kit that enables researchers to develop simulations which may be run as web services and accessed interactively.

The combination of these four technologies resulted in a user-friendly web page where any person can upload cancer-related images and execute analysis algorithms and obtain quantitative measurements related to their images. This figure describes graphically the process of the analysis through CAIMAN.

Graphical description of CAIMAN

More details about CAIMAN, its use and performance can be found in the following paper:
Reyes-Aldasoro, C.C., Griffiths, M.K., Savas, D. & Tozer, G.M. (2010) CAIMAN: An online algorithm repository for Cancer Image Analysis. Comput. Meth. Prog. Bio. in press, doi:10.1016/j.cmpb.2010.07.007.




2) What algorithms are being used?

The algorithms have been specifically developed for each task and some of them have been published. When this is the case, you will have a link to the publisher's website where you can access the publication (depending on the access rights of your institution). In other cases, algorithms have been submitted for publication and we are awaiting the response of the journals.

It is important to remember that every algorithm will assume certain conditions. The shading correcting algorithm, for instance, assumes that an original unbiased image was corrupted by a slowly-varying shading, and that this shading could be estimated from the signal envelope. Then, it is assumed that the objects contained in an image (cells for instance) will be covered by signal envelope (or the background) and that the background is either darker or brighter than the objects. These kind of assumptions will cover a large number of images but there could be an image where there are objects brighter and darker than a background (although this will be more theoretical than practical) and then the algorithm could provide a result that may not be satisfactory.

In summary, algorithms do not work under every imaginable situation, but what they do offer is a consistent processing for all the images they are applied to.




3) Are the results always the same?

The images will be processed by an algorithm, therefore if you submit two identical images, you will always receive the same results. If two images are different, the algorithm will provide consistent results. However, the format of the image though can introduce differences, so if you save the same image as a JPEG or as a TIFF you may have different results for the same image, see below.




4) Does the type of image impact on the results?

Yes. Two images may look very similar to the naked eye, but the format used to save them may impact considerably on the results. Look for instance at these two images, the one on the left is saved as a PNG whilst the one on the right is a JPEG.


PNG Format
JPEG Format



The differences may not be evident but if we zoom in, the sharp red line becomes blurry on the JPEG.



PNG Format
JPEG Format




Therefore, if the images are going to be quantified by an algorithm based on the intensities of the pixels, the format will have an impact. Try to save always with the best quality you can, avoid JPEGs and GIFs which will not be accepted for publications in journals anyway.


IMPORTANT Try to avoid saving images with compression as in some cases Matlab cannot read these images.




5) Is it possible to add more algorithms? Can I propose one experiment to be analysed?

Yes. We are constantly working on new algorithms and there are several algorithms on the pipeline at the moment. If you have an interesting experiment that produces images that require quantitative analysis, contact us and we will study the case. We cannot promise that an algorithm would be produced immediately but we will try. Send an email to (please replace {at} and {dot} when sending the email) c.reyes {at} sheffield {dot} ac {dot} uk or reyesaldasoro {at} gmail (dot) com with a description of your images and the processing required together with one or two example images.



6) Are there any test images?

Yes. you can try CAIMAN with the following images, right click on any to download to your computer.

Migration measurement
Migration measurement 1
Migration measurement 2
Migration measurement 3
Migration measurement 4
Migration measurement 5

Tracing of vasculature
Tracing Vasculature 1
Tracing Vasculature 2
Shading correction
Shading correction 1
Shading correction 2
Endothelial Cell segmentation
Endothelial cell segmentation 1
Endothelial cell segmentation 2
Chromatic Analysis
Fluorescent Cells






7) How long does it take to process an image?

Roughly a few minutes. We have tested with images small (approximately 100 kb or 250 x 200) to large ones (1.5 Mb or 1,200 x 960) and the fastest time from submission to the email being received was 43 seconds, on average it will take more than a minute for shading correction or migration measurements. Tracing vessels takes longer, around3-4 minutes. But the network that you use and the unpredictable internet connections can increase the time.





8) Are there any disclaimers?

Yes, of course! The data and information is provided for educational and informational purposes only, and is not intended for professional purposes. The authors shall not be liable for any errors or responsibility for the accuracy, completeness, or usefulness of any information, or method in the content, or for any actions taken in reliance thereon. If you find any errors or problems with the programs we should try to fix them but no promise is made.









The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK