Loboda, S. | bioRxiv Science

bioRxiv2025

Multi-modal image analysis for large scale cancer tissue studies within IMMUcan

MotivationMultiplexed imaging is increasingly used to study tissue architecture in health and disease. To investigate the cancer tumor microenvironment, typically either tissue micro-arrays or small patient cohorts are used to collect and process data. However, studies performed over the course of years, collecting data from thousands of samples are rare and require specialized workflows to ensure sample throughput and reproducibility for data production and processing. Here, we present two such workflows for multiplexed immunofluorescence and imaging mass cytometry of cancer tissues which are applied to a total of roughly 10000 samples from 2500 patients over six years. SummaryIn cancer research, multiplexed imaging allows detailed characterization of the tumor microenvironment (TME) and its link to patient prognosis. The IMMUcan consortium collects multi-modal imaging data from thousands of cancer patients to perform broad molecular and cellular spatial profiling across five cancer indications. Here, we describe two workflows for multiplexed immunofluorescence (mIF) and imaging mass cytometry (IMC) developed within IMMUcan to enable analysis of thousands of cancer tissues. IFQuant supports web-based, user-friendly, and reproducible analysis of mIF data. High sample throughput for IMC is achieved by optimizing experimental protocols and developing a robotic arm for automated slide loading. We provide a resource of 350000 manually labelled cells across 180 cancer samples to accurately annotate cell phenotypes in IMC. All major cell phenotypes and tissue structures correlate well between mIF and IMC. These pipelines form the basis for multiplexed image analysis within IMMUcan and provide computational tools for the larger community.

cancer biology↗

bioRxiv2020

Taxonomic, temporal, and spatial variation in the dynamics of High-Arctic arthropod populations

Time-series data on arthropod populations are critical for understanding the magnitude, direction, and drivers of abundance changes. However, most arthropod monitoring programs are short-lived and limited in taxonomic resolution and spatial extent. Consequently, variation in population dynamics among taxa and habitats remains poorly understood. Monitoring data from the Arctic are particularly underrepresented, yet important to assessments of species abundance changes because many anthropogenic drivers of change that are present in other regions are absent in polar regions. Here, we utilise 24 years of abundance data from Zackenberg in High-Arctic Greenland, which is the longest running Arctic arthropod monitoring program, to study temporal trends in abundance. Despite a strong warming signal in air temperature, we only find evidence of weak temporal trends in arthropod abundances across most taxa. These trends are more pronounced in the most recent decade, with change point analyses suggesting distinct non-linear dynamics within some functional groups such as predators and detritivores. Although the abundances of many taxa were correlated, we detected both positive and negative correlations, suggesting that multiple processes are affecting arthropod populations even in this relatively simple Arctic food web. Finally, we found clear differences among species within single families of arthropods, indicating that an apparent lack of change in abundance at broader taxonomic or functional levels could mask substantial species-specific trends. Our results reiterate the need for more basic research into the life-history, ecology, and adaptation of arthropod species to better understand their sensitivity to global changes. Significance statementTerrestrial arthropods, including insects and spiders, serve critical ecosystem functions and are excellent indicators of environmental change due to their physiology, short generation time, and abundance. The Arctic, with its rapid climate change and limited direct anthropogenic impact, is ideal for examining arthropod population dynamics. We use the most comprehensive, standardized dataset available on Arctic arthropods to evaluate the variability in population dynamics for the most common arthropod groups at various taxonomic levels across 24 years. Our results highlight that temporal trends of arthropod populations seem less directional in the Arctic than in temperate regions. Although abundances of some arthropod taxa are declining, particularly in recent decades, population trends still display high variation among time periods, taxa, and habitats.

ecology↗