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SchulzDan merged 2 commits into from
Feb 23, 2026
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updated XTi intro #114

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updated XTi intro
SchulzDan Feb 6, 2026
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updated intro
SchulzDan Feb 23, 2026
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33 changes: 33 additions & 0 deletions 01-intro.Rmd
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Expand Up @@ -182,4 +182,37 @@ file.
We refer to this data as raw data and the further
processing of this data is described in Section \@ref(processing).

### IMC instrument generations

In 2023 Standard BioTools<sup><font size="1">TM</font></sup> release the latest
version of IMC machines - the Xti. Compared to the previous generation -
Hyperion - this new generation obtained an extensive makeover. While the
principle of IMC remains the same for this latest generation of machines, many
technical parts have been changed. While this enabled some noteworthy updates,
XTis do not produce TXT files any more. TXT files have previously been used as
recovery files for corrupt mcd files during processing with `steinbock`, and
importantly for spillover correction. To account for this, section
\@ref(spillover_XTi) now contains a paragraph on spillover correction
with data from XTis. The biggest novelty is measurement speed and throughput.
XTis measure at 800 Hz and 1 mm$^2$ is ablated in approximately 25 min.

@alboll-lab alboll-lab Feb 12, 2026

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Maybe it would be interesting to know for users whether the altered speed or new instrument affects signal intensity/sensitivity, so whether the generated data is comparable to the previous machines (based on specifications of StandardBioTools).

@SchulzDan SchulzDan Feb 23, 2026

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added this:
"The XTi has comparable or slightly higher sensitivity than the Hyperion generation. Of note, laser energy titration for ablation is more important on the XTi because ablation with too high laser energy can lead to excessive presence of hot pixels."

Additionally, the process of panorama generation is much faster and whole-slide
panoramas are now recorded in 15-20 minutes. To allow for higher throughput, a
slideloader is commercially available from Standard BioTools<sup><font
size="1">TM</font></sup> enabling batch processing of up to 40 slides. These two
updates now enable throughput of dozens of slides per day thereby allowing
researchers to tackle projects for which no tissue microarrays are available or
feasible.

Besides speed and throughput, XTis also have two additional measurement modes:
1) Pixel-skipping and 2) tissue-mode. Pixel-skipping performs, as the name
implies, lateral and vertical pixel-skipping and in standard settings measures 1
out of 25 pixels in X and Y directions. This enables the generation of
whole-slide images in about 20-30 minutes at low resolution for the purpose of
region of interest selection or pixel clustering or other, relatively unexplored
research questions. In tissue-mode, laser focus and energy are changed and
approximately 5 µm$^2$ spots are ablated. In this mode whole-slide images are
generated in approximately 1-2 hours and they provide better detail than
pixel-skipped data. As of January 2026, no publications are available that made
use of either of these two approaches and it remains to be seen how useful these
measurement modes are.