FAQ

Q What makes Ludesi different from other 2D gel software solutions?
A Ludesi is different from other 2D gel software in the sense that we offer an image analysis service with no software costs at all.

With other 2D gel software you need to do the image analysis yourself, most of the time with questionable results. With Ludesi you get results with guaranteed high Combined Correctness and consequently with guaranteed high discovery potential and low false positive ratio.

To perform the image analysis Ludesi is using its inhouse, proprietary image analysis software system. We also apply the methodology and measurements of Combined Correctness to ensure maximum correctness in your data. This means you get reliable data back.

The difference is that when you use conventional 2D gel software you have no measurement at all of the reliability of your data, or the actual discovery potential, or even error rate. This means that you probably dont have good discovery potential nor low error rate. If you can't measure it, how could you optimize it?

In our experience, from running thousands and thousands of images for hundreds of scientists around the world, most scientists miss out on most of the interesting results when using conventional 2D gel software. Our experience shows that the Ludesi system on average finds 4 times more true positives, and on average decreases the ratio of false positives with 40%, compared to using conventional 2D gel software.

This is probably true for you too. Why dont you give us a try, and see for yourself?

Q Why would Ludesi be any better than my current 2D gel software?
A Ludesi is using a proprietary image analysis system and apply the methodology and measurements of Combined Correctness when your gel images are analyzed.

Combined Correctness has been shown to be strongly correlated to both high discovery potential and low false positives ratio in 2D gel image analysis. So by optimizing the Combined Correctness in the image analysis of your gel images, we can ensure a very high discovery potential and a very low false positive ratio.

You can not do this using any conventional 2D gel software, and this is one of the major reasons to why Ludesi provides better results.

Q What software is being used in the Ludesi Analysis Center?
A The Ludesi Analysis Center is using Ludesi's proprietary inhouse image analysis software. The Ludesi image analysis software system has proven to be far superior to any commercial avialable 2D gel software, as shown in numerous direct comparisons with our customers.

If you are interested, please contact us and we will be happy to provide you with satisfied reference customers, that will testify on our quality and effectiveness.

Q Can you also run gels for me?
A No, we dont have any gel running capabilities. We however collaborate with selected proteomics companies who can offer this type of service. Feel free to contact us with your request, and we will recommend you a suitable partner for your project.

Q Can you also give me identifications on my protein spots?
A No, we dont have any mass-spectrometry capabilities. We however collaborate with selected proteomics companies who can offer this type of service. Feel free to contact us with your request, and we will recommend you a suitable partner for your project.

Q In what format do you need the 2D gel images?

A We need the images in .tif or .gel format. It is preferred to use 16-bit grayscale images. The resolution should be great enough so that even the smallest protein spots are not overly pixilated. A good resolution is usually between 150 and 350 dpi. You should be careful about doing any sort of manipulation of the images in programs such as Photoshop. Doing this puts you at risk of losing or distorting information unless you are certain of what you are doing.

Q What is "DPI" and "bit depth" and what settings should I use in order to optimize my image analysis results?
A DPI -"DPI" means "dots per inch" and is a measure of resolution in your gel image file. Normal DPI values for 2D gel images range between 150 and 400 DPI, but this is highly dependent upon the size of the gel. The important thing is to make sure that the smallest spots are not too pixilated when you zoom in on them in the image. If you zoom in on the smallest spots in your gel and they still look acceptable you are probably fine.

Sometimes "dots per centimeter" is used. 1 DPC is equal to 2.54 DPI.

BIT DEPTH - The "bit depth" is the number of binary bits containing information about the intensity value in each pixel in your gel image file. Common bit depths in grayscale images are 8 bits, 12 bits and 16 bits. Having 8 bits means a range of 2^8 = 256 possible values in your grey scale. Having 12 bits means 4,096 values, and 16 bits means 65,536 possible values in your image.

Try to scan your gels in a high bit depth, preferably 16 bits. The images are still analyzable at 12 or 8 bits, but having 65,536 grey levels is more sensitive than having 256 grey levels for each pixel and therefore makes the analysis results more reliable. However, not all scanners are able to output 16 bit images.

A 16 bit file uses twice as much memory as an 8 bit file, but has 256 times as many grey levels. The extra accuracy provided by a 16 bit image is usually well worth the increase in file size.

Q You have previously analyzed a set of gel images for me, and now I have a set of new images that I want to have analyzed together with the previous gel images. Can you do that?
A Yes, that is possible, and we can retain the same protein ID numbers as in the previous project. Please contact support@ludesi.com for more information on the various options regarding this, and the cost involved.

Q Can you provide me with picker files to use in our spot picker?
A Yes, we can create picker files to be used in various spot picker robots. Please contact support@ludesi.com to have this arranged.