Apex

From Northwestern University Center for Atom-Probe Tomography

Apex
Apex a22, showing a 1D cylinder composition profile
Maintainer	Olof Hellman
Latest release:	alpha-41 / May 31, 2006
OS:	Mac OS X
Genre:	Atom-Probe Tomographic Analysis
License:	By arrangement with Olof Hellman
Website:	http://www.tomographic.com/

Apex (Atom-probe experience) is a Macintosh OS X program developed by former Seidman-group member Olof Hellman under his company "Tomographic Softworks ^[1]." Apex runs on all of the NUCAPT macs and some of the personal machines of individuals in the Seidman group. Please contact Olof directly if you'd like to use Apex on your non-NU computer.

Contents 1 System Requirements 2 Features 3 References 4 News

[edit] System Requirements

A mac with a G4 or G5 processor and OS X 10.3.9 or later is recommended. Apex can run on OS 10.3.8 and earlier versions of 10.3, but you will need to install libstdc++ version 6.0. However, the easiest way of doing this is to upgrade (for free) to version 10.3.9. The more memory the better, but at least 512 MB is recommended. In addition, one should have sufficient free disk space. As a rule of thumb, at least 100 bytes of free disk space per ion in a dataset you wish to work on – If you have a dataset of 2 million ions, try to have 200MB of free disk space. NUCAPT has a dual-2.7 GHz G5 with 8 GB of RAM and plenty of disk space to run Apex.

[edit] Features

• Adjustable isoconcetration surfaces^[2]
• Proxigram^[3][4]
• Imports:
  • .pos (standard for many atom-probe groups)
  • .ops (used by the Oxford group)
  • .dat files (used by the Rouen group)
  • .atomlist files (originally used by the Northwestern group with the 3DAP)
• Exports:
  • .pos
  • .atomlist
  • .ato (wide data / Rouen format)
• Manipulation via
  • GUI
  • Applescript

[edit] References

1. ↑ Hellman, Olof; Vandenbroucke, Justin; Blatz du Rivage, John; Seidman, David N. (2002). "Application software for data analysis for three-dimensional atom probe microscopy". Materials Science and Engineering A 327 (1): 29-33. doi:10.1016/S0921-5093(01)01887-1. 
2. ↑ Hellman, Olof C.; Blatz du Rivage, John; Seidman, David N. (2003). "Efficient sampling for three-dimensional atom probe microscopy data". Ultramicroscopy 95 (May-June): 199-205. doi:10.1016/S0304-3991(02)00317-0. 
3. ↑ Hellman, Olof C.; Vandenbroucke, Justin A.; Rusing, Jorg; Isheim, Dieter; Seidman, David N. (2000). "Analysis of Three-dimensional Atom-probe Data by the Proximity Histogram". Microscopy & Microanalysis 6 (5): 437-444. doi:10.1007/s100050010051. 
4. ↑ Hellman, Olof C.; Rusing, Jorg; Sebastian, Jason T.; Seidman, David N. (2001). "Atom-by-atom chemistry of internal interfaces: simulations and experiments". Materials Science and Engineering C 15 (1-2): 13-15. doi:10.1016/S0928-4931(01)00224-7. 

The calculation of the Gibbsian interfacial excess is described in:

Hellman, Olof C.; Seidman, David N. (2002). "Measurement of the Gibbsian interfacial excess of solute at an interface of arbitrary geometry using three-dimensional atom probe microscopy". Materials Science and Engineering A 327 (1): 24-28. doi:10.1016/S0921-5093(01)01885-8. 

[edit] News

Tomographic Softworks

Apex a48 is live (14.Mar. 01:21)

The first update in a long time. This includes the planes UI I screencasted a few days ago, and plenty of other new bits in the UI and under the hood. The conversion away from DITL resources over to Interface builder nibs is complete. I’ll be screencasting more in the next few [...]

Screencast demo of the new planes feature (12.Mar. 04:24)

Here’s a screencast I did showing the new UI for manipulating and exploring planes. There’s a high resolution version on Viddler, which really works great in full screen mode. When embedded in another page, like this YouTube link, its hard to see what’s on the screen. I’ll be releasing [...]

An Introduction to Using Apex (08.Mar. 23:35)

Here’s a step-by-step intro to some first steps with Apex. I’ll be trying to add content to this document as I am able. UsingApex.pdf

Moved the Blog to WordPress (08.Mar. 22:18)

This blog previously lived here: http://homepage.mac.com/olof/tomographic/ Where the links should still be active. I’m trying to move the old content over here to WordPress.

A Movie Example (08.Mar. 22:16)

Here’s a movie I made to show off some of the 3D graphics of Apex. The rotation sequence is produced from a script — the other bits are screengrabs from Apex with different atoms visible in the display. Its all thrown together with iMovie with a voiceover I recorded late one night, so I sound [...]