AtomProbeLab / Blog: Recent posts

This version fixes a simple but important bug in the recently updated background subtraction code.
It also tries to handle rank deficient problems, where there isn't actually enough information to solve the problem, with a little more grace. You will get an answer but it should have a huge confidence interval. This is a problem if you run the calculation without confidence intervals - you won't see there is an issue. However, when you build the overlap problem you will get a handy warning that the problem cannot be solved, so you've been warned! I hope to add some other message in the future, or maybe make the estimated compositions NaN - there is literally no way to solve this overlap. Here's an example where Al+ and Al++ overlap, the Al/Al2 overlap cannot be solved, but the composition of Fe and Cr is correct (48 at% for both) even though they are part of the same overlap group:... read more

Mostly just minor fixes, including an important fix for massOverlapSolver. The residual counts were being included in the composition calculation, so compositions of real species would not sum to 100%.
Also added a new labelling function to massSpectrumPlotter to render ion labels above the spectrum to added clarity.

Quite big changes under the hood to massOverlapSolver and getRangeCounts that allow you to solve multiple sub-volumes within a single data set. See the demoScript_bulkDecompParts script for a demonstration. Still working out how to handle the output and how it should be formated, so expect some changes in future versions.

Another quick bug fix version for single-ion overlap solving. Still working on decomp-parts..!

Very small but important fix for local peak solving has been made. This now allows overlaps of more than 2 ions to be solved. I expect to be reworking the local-decomp code to use the new "overlap problem" struct that the bulk-decomp method uses in the near future. First, I'm working on bulk-decomp parts: so that one data set can be split, using some kind of index, into multiple parts and each part have its overlaps solved separately.

After many small fixes, especially for the peak-overlap solving code, AtomProbeLab has been updated to 0.1.0! Future bug fixes will be 0.0.x level and more major changes 0.x.0.

While hopefully the accuracy of the overlap solving code should not be changed, there was a bug with adding additional ions with elements not defined in the range file which may have altered the returned results. If you add ions to your overlap problems, then please double check your results using the new version of the code.... read more

Peak-overlap solving for "bulk" datasets is now here!
Bulk means a pos-file or list of m/z values, so it could be as big or as small as you like. The new overlapProblemBuilder lets you formulate your overlap problems, populate it with range counts using overlapProblem_getRangeCounts and then solve your overlaps using massOverlapSolver. Visualise the output and share your overlaps using overlap graphs rendered using dot.exe via overlaps2graphviz_colour2. There are a lot of new functions, so expect things to change over time as there is constructive feedback.

There as been a lot of shuffling behind the scenes. Everything should work as before, with some much needed fixes, and the AtomProbeLab folder looks a lot cleaner. All of the m-files which make up APL have been moved into a folder called "/src", so when you want to use them simply add:

addpath('src\');

to your script and you will be able to access the goodies within.

Stay tuned for a big release with a bulk peak overlap solving function coming soon!

A bug has been fixed in the method used to generate the local surroundings. In the previous version the origin atom was included, this could cause composition biasing effects. I would recommend if you had any important analyses that you re-do them with the new software.

The very first version of AtomProbeLab has been published. This is still very much in development, but should contain all the tools necessary for performing single-ion peak deconvolution of atom probe data. Watch this space for future developments.