Image processing programs for microscopy

Image processing programs are so numerous that it is a daunting task to find one that is easy to use, and also provides the basic filters and effects that microscopists (thinking here specifically of those that use TEM, and AFM, the only two with which i am familiar). All the commercial tricks for graphic design are not helpful in enhancing images and data (such as smoothing LUT plots of brightness and contrast, to sharpen edges, and increase the chances of quantifying “real” events.

In a search for affordable (and often free and dedicated) user friendly programs for processing images I have used my own “artificial” image of solid squares and circles (RGB) as well as “real” images from several types of published and original micrographs of two well studied multimers (surfactant protein D and DMBT1 –  from various species).  I do NOT in any way profess to understand the math behind various signal processing libraries used in any of these programs. I only express opinions about how they affect my the images, and enhance retrieval of data that can be otherwise be missed.

What follows is just my opinion but it might provide insight for someone who just wants to find an easy program and use the basic filters and effects,  and it might help someone who wants to use such filters and effects to investigate molecular structure of a particular molecule.

The programs whose filters and effects I studied pretty thoroughly, paid, and free  opensource, and an estimate of how easy it was to process the images and “real” images are to the right. First on the list is CorelDRAW which is a program I have used for almost 3 decades, and Photoshop for almost that long. Both are paid programs that have extensive menus of filters and effects, way beyond what is  practical (and pertinent) for image processing for scientific work. It is difficult to assess the ease of use of those two programs because of their long history and general familarity.  Their effects and filter menus are easy to find and extensive. Their affordability has made them less practical now.

Some institutions provide Adobe licenses for their faculty, staff and students, though a two month personal subscription to Photoshop2021 provided me with enough time to process hundreds of images to compare with earlier Photoshop versions. That said, many of the filters for image processing have not changed in decades either.

Features to look for are those which adjust — the  size, color management (HSL, RGB,  and provide the standard filters and effects, e.g. gaussian blur and median, maximum, minimum, highpass, noise and unsharp mask filters.

CorelDRAW (includes CorelPhotoPaint): There are two ways to process images in Corel. 1) is built into the vector part of the program (CorelDRAW) that has all the most commonly used and relevant filters for image processing.  The separate raster processing portion (CorelPhotoPaint) has a different feel than Photoshop but also has the necessary filters to process images. I have found that CorelDRAW (under current owners) has begun very aggressive popup tactics that are not only annoying but sometimes crash the program.  The current commercial version of Photoshop is really only available on a monthly  subscription.

GAUSSIAN BLUR IS A GREAT FILTER – number of pixels to select depends upon the ppi of your image and your desired effect. All programs above have a blur filter.

This I confirmed when I compared images processed in programs separated in time by at least 10 years. Picking up an old CD of CorelDraw (which includes CorelPhotoPaint) or Photoshop is really pretty sufficient for any processing of TEM or AFM images that one needs and has filters that are similar (or nearly identical) across platforms and time. The algorithms used for these standard filters seem to be part of a library and accessible to programmers creating their own image processing platforms, so there is an underlying uniformity among them all (not withstanding some variations, limits, menu name changes, and the addition of sliders for adjusting levels of filter application.

The order in which filters are applied matters as does the pixel radius relationship of each applied filter and percent applied.  Vector image exported to 300ppi tif (8″ width), imported into CorelDrawx5 and processed –bitmap>sharpen>highpass 50% 10px, then – blur>gaussian blur 3pxr, (left image); or bitmap>blur>gaussian blur 10pxr, then highpass 50% 10px (right image). Bottom image, blur>gaussian blur 3pxr, then highpass 50% 10px.
THE ORDER OF APPLICATION of the filters matters in the cosmetics of the outcome, and may affect outcome.