Cellular & Molecular Imaging

A reference dataset containing macroscopic and bright-field microscopic images of 16 specimens of thallose liverworts of biological soil crusts collected in Southern Sweden and Germany

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. This is a collection of the samples included in the study, provided by COPO at Earlham Institute.

Differentiation of induced pluripotent stem cells (iPSC) towards different neuronal lineages has enabled diverse cellular models of human neurodevelopment and related disorders. However, in vitro differentiation is a variable process that frequently leads to heterogeneous cell populations that may confound disease-relevant phenotypes. To characterize the baseline and diversity of cortical neurodevelopment in vitro, we differentiated iPSC lines from multiple healthy donors to cortical neurons and profiled the transcriptomes of 60,000 single cells across three timepoints spanning 70 days. We compared the cell types observed in vitro to those seen in vivo and in organoid cultures to assess how well iPSC-derived cells recapitulate neurodevelopment in vivo. We found that over 60% of the cells resembled those seen in the fetal brain with high confidence, while 28% represented metabolically abnormal cell states and broader neuronal classes observed in organoids. Further, we used high-content imaging to quantify morphological phenotypes of the differentiating neurons across the same time points using Cell Painting. By modeling the relationship between image-based features and gene expression, we compared cell type- and donor-specific effects across the two modalities at single cell resolution. We found that while morphological features capture broader neuronal classes than scRNA-seq, they enhance our ability to quantify the biological processes that drive neuronal differentiation over time, such as mitochondrial function and cell cycle. Finally, we show that iPSC-derived cortical neurons are a relevant model for a range of brain-related complex traits. Taken together, we provide a comprehensive molecular atlas of human cortical neuron development in vitro that introduces a relevant framework for disease modeling.

In Drosophila male gonads, niche-derived Decapentaplegic (Dpp) has a role in maintaining stem cells in close proximity but the range of Dpp diffusion and its role has never been tested in the differentiating cells spaced one-cell layer away. Here, using genetically encoded nanobodies called Morphotraps, we physically block Dpp diffusion without interfering with niche-stem cell signaling and find that a diffusible fraction of Dpp is required to ensure differentiation of GSC daughter cells, opposite of its role in maintenance of GSC in the niche. Our work provides an example in which a soluble niche ligand induces opposed cellular responses in stem cells versus differentiating descendants to ensure spatial control of the niche, which may be a common mechanism to regulate tissue homeostasis.

The Darwin Tree of Life project has the goal to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland. This is a collection of photographs of the samples included in the study, provided by the National History Museum (NHM).

The following data includes raw images, metadata, measurements and processed images as well as classifiers for image segmentations and masks created with the ImageJ/Fiji plugin Labkit to measure the leaf area. This dataset provides all acquired information for my Bachelor's thesis about leaf traits of Bryophyta related moss species.

Chlamydomonas smithii exhibits remarkable morphological plasticity (pleomorphism) in response to environmental conditions. This dataset captures the diverse cell shapes and subcellular structures observed when C. smithii cultures are maintained under nutrient-depleted conditions over extended periods (40-43 days). We examined cells grown on multiple media types (Marine Broth, Erdschreiber's Medium, Kuhl's Medium, TAP, and water) supplemented with 1.5% agar, resuspended in liquid growth media, and applied various fluorescent stains (FM4-64 membrane stain, MitoTracker Orange, PKmito Orange) to visualize subcellular compartments. The dataset includes brightfield, RGB, and fluorescence z-stack images capturing the wide range of pleomorphic forms that emerge during prolonged culture, including multi-lobed cells, enlarged vacuoles, and altered chloroplast morphologies.

Using lacZ reporter mouse models, we mapped expression of the HH ligand SHH, HH receptors, and GLI transcription factors in fungiform, circumvallate and foliate taste papillae in early and late postnatal and adult stages. In adults we also studied the soft palate, and the geniculate and trigeminal ganglia, which extend afferent fibers to the anterior tongue.

We used Chlamydomonas reinhardtii motility mutants with disrupted genes homologous to human SPEF2 or DNALI1 to model spermatogenic failure disorders SPGF43 and SPGF83, respectively. We recovered aspects of wild-type motility in these mutants with a small-scale drug screen.

Motility is a phenotypic readout that indicates an organism’s integration of sensory input from its environment with its ability to move. We developed a microscopy workflow and image analysis pipeline to track motility phenotypes from unicellular algae in high-throughput.