diff --git a/01-intro.Rmd b/01-intro.Rmd index 3ba53df..6420ecb 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -182,4 +182,41 @@ 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 BioToolsTM 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. The XTi +has comparable or slightly higher sensitivity compared to a machine of the +previous generation. Of note, laser energy optimization is more important on the +XTi because ablation with too much 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 BioToolsTM 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.