From 6ca4cae0cbfa29c2a5a8d2d006e1fc13e0dd2290 Mon Sep 17 00:00:00 2001 From: SchulzDan Date: Fri, 6 Feb 2026 12:39:24 +0100 Subject: [PATCH 1/2] updated XTi intro --- 01-intro.Rmd | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/01-intro.Rmd b/01-intro.Rmd index 3ba53df..486a18f 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -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 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. +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. From caa48efd2a518c7270a746cfc714c9b2cdf1b3dc Mon Sep 17 00:00:00 2001 From: SchulzDan Date: Mon, 23 Feb 2026 11:16:03 +0100 Subject: [PATCH 2/2] updated intro --- 01-intro.Rmd | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/01-intro.Rmd b/01-intro.Rmd index 486a18f..6420ecb 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -194,7 +194,11 @@ 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. +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 BioTools