Image SXM FAQs

FAQs - Frequently Asked Questions

Listed below are some of the questions that have been emailed to me over the past 15 years. Strictly speaking, only a few of these can be called FAQs as many have not been asked frequently -- most are one-off questions that relate to a specific situation that a user has encountered. Even so, I think that the questions and the answers listed below may be of general interest to other users. The questions have been grouped into loose categories, but are otherwise in no particular order.

Versions and Code: Is there a version of Image SXM that runs natively on Intel Macs?; Is there a version of Image SXM that runs on a PC/Windows/DOS/Linux?; Is Image SXM public domain? Is it freeware? Is it shareware?; Is the source code for Image SXM in the public domain?; Is the source code for Scion Image for PCs available in the same way as NIH Image for Macs?

Users and Citations: Is there any email list of SXM users?; How should Image SXM be cited in publications?

Program Settings: How much memory should I allocate to Image SXM?; Do I have to explicitly save the preferences before quitting?

Image Processing: Does Image SXM automatically adjust the greyscale so that the full range of greys are used?; Can I select a ROI to define a subtraction plane, and then subtract that plane from the whole image?; Does Image SXM do some kind of background removal from images when they are loaded?; Does the compensation function alter the real dimensions of the image?; Is it possible to change the z scale of an image while maintaining its calibration?; Is there a way to create my own LUT?

Image Analysis: Can I save the profile plot as data points and then plot it in a spreadsheet application?; Can I get a height histogram of my particles?

General: What are the new features of Image SXM v1.xx compared to v1.xx?; Is there a way of saving files in xxx format?

Versions and Code

Q: Is there a version of Image SXM that runs natively on Intel Macs?

A: The current version (as of July 2015, this is v198) runs natively on Intel Macs.

Q: Is there a version of Image SXM that runs on a PC/Windows/DOS/Linux?

A: No, Image SXM is an Apple Macintosh application. The source code is 150,000 lines of Pascal code. Rewriting it to run under Windows would require me to give up all of my spare time for the next few years, which I am not prepared to do. It would also require me to buy a PC and learn how Windows works. This I am definitely not prepared to do.; If you really want to run Image SXM on your PC, then you can use a Mac emulator such as PearPC or Executor or Basilisk II to run under Windows or Linux. PearPC emulates a G4 PowerPC processor and will run the latest version of Image SXM. With the other emulators, you will need an older version of Image SXM (see the Installer Archive page). Image SXM will run an order of magnitude slower than on a Mac, but users have reported that it does work OK.

Q: Is Image SXM public domain? Is it freeware? Is it shareware?

A: Image SXM is a version of the public domain application NIH Image and is distributed freely to anyone interested in using it. Image SXM is not public domain because the source code is not distributed with the application (this is part of the definition of public domain).

Q: Is the source code for Image SXM in the public domain?

A: No (see above). If you are interested in using the source code of Image SXM to develop a specialist application of your own then email me.

Q: Is the source code for Scion Image for PCs available in the same way as NIH Image for Macs?

A: "The source will not be made available." <support@scioncorp.com>

This makes it impossible for any user to adapt or extend Scion Image to create the equivalent of Image SXM for PCs.

Users and Citations

Q: Is there any email list of SXM users?

A: Not a separate one -- the NIH Image list serves users of Image SXM and Object Image in addition to NIH Image.

Q: How should Image SXM be cited in publications?

A: I would prefer that it is cited with the following phrasing in the text:
: The image processing and analysis was carried out using Image SXM [ref] ...
: and in the references listed at the end of the publication:
: [ref] Image SXM, Steve Barrett (2015) http://www.ImageSXM.org.uk

Program Settings

Q: How much memory should I allocate to Image SXM?

A: For Mac OS 9; The default settings should be OK for most users. If you intend to load large images (> 1 Mb) or many images (> 100) or you have a large number of Undo levels (> 10) then you may need to allocate more. Set the Undo and Clipboard buffers to the maximum image size that you normally handle. Set the memory allocation of Image SXM using 'Get Info' in the Finder to

(max image size) x (max number of images loaded at any time + Undo levels) + 10 Mb: A: For Mac OS X; Memory is not allocated to applications in the same way that it is under Mac OS 9. Every application running under OS X has access to 2 Gb of memory, and OS X uses virtual memory to share the actual memory between all active applications and other processes.

Q: Do I have to explicitly save the preferences before quitting?

A: In general, yes. The 'Image SXM Prefs' file is not saved whenever you change one of the options in a dialog box. If the changes were saved automatically, then you would have to remember to set them all back the way they were if you wanted to start with your preferred settings next time you used Image SXM. The exception to the rule is changing the size of the Undo and Clipboard buffers, which will save the preferences file and then inform you that changes will take affect after Image SXM is quit and relaunched.

Saving the preferences is achieved by hitting the 'Save Prefs File' button in the SXM Prefs dialog box, or by selecting the 'Record Preferences' menu item.

Image Processing

Q: Does Image SXM automatically adjust the greyscale so that the full range of greys are used?

A: Yes, this is the default behaviour. When reloading images with compensation for tilt or curvature over a user-selected region of interest (ROI), the default look-up table (LUT) is the same as for the original image. You can override this by (i) pressing the option key to increase the contrast so that the full range of greys is used within the ROI, or (ii) pressing the shift key to decrease the contrast so that all of the levels of the reloaded image lie within the LUT.

Q: Can I select a ROI to define a subtraction plane, and then subtract that plane from the whole image?

A: Yes. Select the region of interest (ROI), then select 'XY Tilt Compensation' from the compensation submenu. The plane will be subtracted from the whole image. The LUT will be the same as for the original image, unless the option or shift keys are pressed (see above).

Q: Does Image SXM do some kind of background removal from images when they are loaded?

A: By default, Image SXM applies an xy tilt compensation when loading SXM images. If you would prefer to see the raw images (and apply compensation to images manually), this can be switched off from the 'SPM Options' dialog box.

Q: Do the compensation functions alter the real dimensions of the image?

A: No. The compensation functions are designed to remove constant, linear or quadratic functions (lines or planes) from the image data to make it easier to see or measure features in the image. The apparent height of any feature in the image remains the same, even though the number of z levels displayed in an image that has been compensated for tilt or curvature may not be the same as that of the raw (uncompensated) image.

Q: Is it possible to change the z scale of an image while maintaining its calibration?

A: One of the simplest methods is to use the controls in the Map window to change the mapping between z values and greyscale. Use 'Apply LUT' to fix the greyscale according to the settings you have set. The z calibration will be maintained. Alternatively, you can use 'Match LUTs' to ensure that all open images have the same mapping between z values and greyscale, or 'Change LUTs' to specify the z values that you would like to correspond to the black and white levels of the image. These are described in the 'Image SXM Help' pages.

Q: Is there a way to create my own look-up table (LUT)?

A: This can be done in a number of ways:

(i) Edit a LUT using the eyedropper tool -- double-click on a colour in the LUT window to set that colour.

(ii) Edit a LUT using the LUT tool (the double-headed arrow) -- change the colours by click-dragging in the LUT. With the option key pressed, click-dragging will 'rotate' the colours through the LUT.

(iii) Import LUT data from a file -- select 'Look-Up Table' from the 'Import' dialog box to import a 768 byte binary LUT consisting of 256 consecutive red values, 256 consecutive green values, and 256 consecutive blue values. The values should be in the range 0-255.

(iv) LUT data can also be loaded from text files (where the LUT values have been generated using a spreadsheet). Email me for details if you are interested in how to do this.

The custom LUT can be saved to a binary data file using 'Export', or saved as a menu item by pressing the option key and selecting 'Options > Color Table > Save Digital Instr >' and any of the 26 custom colour tables.

Image Analysis

Q: Can I save the profile plot as data points and then plot it in a spreadsheet application?

A: Yes, export the Profile Plot data using 'Export' from the File menu. The export format is set to 'Plot Values' by default if the front window is a Profile Plot. You can open the exported data file and use copy-and-paste, or import the exported data file into your spreadsheet application.

Q: Can I get a height histogram of my particles?

A: Yes. After carrying out particle analysis in the usual way, press the option key and select 'Analyze Results' from the Analyze menu.

General

Q: What are the new features of Image SXM v1.xx compared to v1.xx?

A: The complete history of the changes that I have made to every version of Image SXM is archived in the History web pages and also in the documentation folder of every release of Image SXM.

Q: Is there a way of saving files in xxx format?

A: Although Image SXM supports about 50 file formats for loading SXM image files from various manufacturers, it does not use these file formats for saving images. Ensuring that the structure of file headers is correct and complete, so that the saved images could be loaded back into the original manufacturer's software without causing any problems, would be extremely difficult and time consuming, especially for so many different formats.

Steve Barrett July 2015

S.D.Barrett@liv.ac.uk

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