Lam, C. Y. | Search bioRxiv

bioRxiv2025

Automated registration of spatial expression data scales multimodal integration to large cohorts

Recent advances in spatial proteomics enable quantification of the spatial distribution of protein expression across a variety of scales, resolutions, and multiplexing. Registering images from such technologies across modalities is an essential task that enables both the integration of complementary imaging technologies and validation of biological findings. This can be particularly challenging when the modalities capture fundamentally different types of data, such as light intensity, probe counts, or heavy metal counts. However, few datasets and methods address this problem at scale. Here, we introduce the largest dataset to date of cross-modality imaging of both cell line and tissue slides suitable for benchmarking registration methods. We further present Twocan, a Bayesian optimization framework that enables robust automated registration between immunofluorescence imaging and highly multiplex spatial proteomics data. Our method achieves significantly higher registration success rates compared to existing approaches across our comprehensive dataset of 954 image pairs.

bioinformatics↗

bioRxiv2019

Sexual dichromatism in the neotropical genus Mannophryne (Anura: Aromobatidae)

Recent reviews on sexual dichromatism in frogs included Mannophryne trinitatis as the only example they could find of dynamic dichromatism (males turn black when calling) within the family Aromobatidae and found no example of ontogenetic dichromatism in this group. We demonstrate ontogenetic dichromatism in M. trinitatis by rearing post-metamorphic froglets to near maturity: the throats of all individuals started as grey coloured; at around seven weeks, the throat became pale yellow in some, and more strongly yellow as development proceeded; the throats of adults are grey in males and variably bright yellow in females, backed by a dark collar. We demonstrated the degree of throat colour variability by analysing a large sample of females. The red: green (R:G) ratio ranged from ~1.1 to 1.4, reflecting variation from yellow to yellow/orange, and there was also variation in the tone and width of the dark collar, and in the extent to which the yellow colouration occurred posterior to the collar. Female M. trinitatis are known to be territorial in behaviour. We show a positive relationship between throat colour (R:G ratio) and escape performance, as a proxy for quality. Our field observations on Tobagos M. olmonae showed variability in female throat colour and confirmed that males in this species also turn black when calling. Our literature review of the 20 Mannophryne species so far named showed that all females have yellow throats with dark collars, and that male colour change to black when calling has been reported in eight species; in the remaining 12 species, descriptions of males calling are usually lacking so far. We predict that both dynamic and ontogenetic sexual dichromatism are universal in this genus and provide discussion of the ecological role of dichromatism in this genus of predominantly diurnal, non-toxic frogs, with strong paternal care of offspring.

zoology↗