H&E Image Optimizer - A Student Project

Most pathologists present digital images to various audiences. For those in academic centers this becomes one of their duties. It is, however, unrealistic and unfair to expect them perform like experts in the image processing arena. Interested colleagues can, without doubt, make certain operations on their images using a variety of software tools. This humble project does not aim to compete with that kind of expertise.

The aim is, in short, to provide a lightweight and easy-to-use computer program to help people with

• little image processing experience
• a less than perfect H&E image, and
• little time.

The tool tries to do two things:

1. Optimize the illumination
2. Sharpen the image.

Optimize Illumination

This is most helpful for images with uneven lighting (poor Koehler illumination, technically) for which you can see an example below. This is not available -in this form, at least- in many commercial image processing applications. For images with already nice lighting you may not see any change at all. This option requires your interaction by clicking on area(s) you want "white". For images without any "white area" the tool can only make an educated guess. The "optimize illumination" feature is not Hematokxylin & Eosin (H&E) specific; so, you may try it on your other images (including touristic ones). But remember that it works pixel-by-pixel and processing a high resolution image may take some time... This is particularly so if you start optimization without selecting any point. This choice is provided only for images that did not contain patches of white.

Sharpen

The second option of the tool comes without bells&rings. It "sharpens" your image a little bit. Some of you may ask what is so special about this as the function is so widely available. Well, it actually tries to sharpen the "blue" objects (most likely nuclei) preferentially. For most images it accomplishes this; for some, there may be no noticeable change. Certainly, it cannot make a beautiful image better. This tool is designed to make poor images acceptable. Actually, no software manipulation is likely to produce a better picture than an already perfectly shot one. So if you have time and resources, go take a better picture of the slide you want to show to others. If not, you may just be looking at the right place! If the increased sharpness (which may cause a pixellation effect) looks irritating, try lowering the amount of sharpenning. (For the technically minded, the function does an "unsharp mask" on the bluish pixels using the Lab color model). To see whether the image indeed got better, re-open the original image and select "Tile" (horizontally or vertically) from the "Window" menu. You can then compare the original and the modified images side by side.

A Tip

The results of "Optimize Illumination" are heavily dependent upon where you click on the image. If you do not find the optimized image suitable for your taste, try repeating it (after an "undo") with more or less clicks on different areas. The same also applies to the degree of sharpenning; some images may become irritatingly pixellated while others may look just the same after this procedure. Try repeating the procedure (after an "undo") by playing with the related slider. Please reserve the words nice boys&girls should never utter, until after a couple of unproductive trials!

Examples

Below are examples to give you an idea about what you may expect from this utility. (More than 800x600 pixels monitor area may be required for proper view). Auto Contrast and Auto Levels are automatic adjustments made using a popular commercial image manipulation package. There is no doubt, however, experts can make better adjustments. Note especially the better handling by H&E Optimizer of the poor Koehler illumination seen in the second row. (Four points close to corners have been selected).

The first raw contains an image of post-chemotherapy osteosarcoma; the second is from a liver adenoma. The images were reduced from 768 x 576 pixel originals.

Original image	Auto Contrast	Auto Levels	H&E Image Optimizer

Below is the result of the "Auto exposure" feature of another popular software. Note the inconsistent and unexpected nature of the results.

Auto Exposure 1	Auto Exposure 2

User interface

The user interface is simple. No detailed help is yet available. Return this page when necessary or send one of us an e-mail.

Printing

The tool is designed and tested for images to be presented on computer monitors and data projectors. It way well contribute to printing. However, we have not tested its performance in modifying images for printing. If you do so, please send us a note and share your comments. (Also, please remember to submit only 300dpi images for printing).

Platform&Download

The tool runs on computers with one of Mr. Bill Gates' operating systems (widely known as Windows ^TM) installed. Although the program itself is small, processing big files (thousands of pixels wide) may take some time. You may still give it a try even if this is the first time you hear about "pixels"!

The software itself is quite small and easy to download. However, in some computers a lack of some critical files (*.dll's) may prevent proper operation. Unfortunately, more computers are in this category. In this case, a larger package must be downloaded which contains all the -potentially- missing system files. Below are the two versions:

• H&E Optimizer 0.9a1.
(110KB) This is a compressed executable. After download, you just double click on it to work. The only limitation is its lack of support for the TIFF format. You can, of course, convert your files into "jpeg" using other tools and use H&E Optimizer afterwards. This version is also for those who just want to have a look into this software. There is no uninstall; if you do not like it you just delete it. The software does not change any of your settings and leaves no traces if you delete it. This is an updated version (...a1) of the original program in response to requests from its first users; our thanks to them...
• H&E Optimizer 0.9b.
(3.8MB) This download contains not only the executable, but also some "dll" files as well as support for other image formats including TIFF. It is a Windows program with installation and uninstallation facilities available. This version is for those who need TIFF support and for those whose system cannot use the above version for lack of certain files. (The name of a missing file may appear in error messages). This version is a response to users who reported difficulties due to lack of a system file or another in their systems. We are thankful for their trials.

H&E Image Optimizer does not contain any virus or bacteria, even though it had been produced under non-sterile hospital conditions!

A Note of Caution

In spite of all you have read here, please do not forget that this is not a high-end image manipulation software. It is just an attempt to help solve a little problem faced by most of us. The program -although itself small- may be very memory-intensive and may make computers with modest amounts of RAM (64 MB and below) unresponsive for a minute or two. It is however, very unlikely that H&E Image Optimizer might cause a black smoke coming from either behind your monitor or from your PC :)

User Comments

All comments are very much appreciated. The software may be updated and its perfomance can be increased if and when there are users showing an interest in its use. The comments will be shared with the visitors to this site. (All personal information will be removed before placing user messages here).

Credit, Licence etc.

The software was written entirely by Mr. Kaya Kuru to fulfill a requirement during his course for a degree at The Institute of Informatics at The Middle East Technical University, Ankara, Turkey. Assoc. Prof. Erkan Mumcuoğlu was his director. The idea of producing an image processing application for this purpose came from Bülent Celasun, MD, a pathologist.

The software is entirely free for personal and educational use. (See:GPL) Commercial use is neither intended nor allowed.