Cellular & Molecular Imaging

TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen Trypanosoma brucei by endogenous tagging with mNeonGreen (mNG). This deposition includes the localisations, ontology and microscopy data used to build the TrypTag database. Data can also be browsed at TrypTag.org. If you use this data resource please cite Billington et al. 2023 Nature Microbiology (doi:10.1038/s41564-022-01295-6). We recommend including this citation in the results or methods if TrypTag was used as part of a discovery process. If directly using TrypTag images, please also indicate in the figure legend or similar which images are from TrypTag. If carrying out a large-scale data analysis, please also cite this BioStudies deposition. Data can be mined via the cellular localization imaging or cellular component GO term searches at the genome database TriTrypDB.org (part of VEuPathDB). If you do, please also cite the genome database. You may also find the following papers informative: Dean et al. 2016 Trends in Parasitology (doi:10.1016/j.pt.2016.10.009), which describes the original project aims and workflow. Halliday et al. 2019 Molecular and Biochemical Parasitology (doi:10.1016/j.molbiopara.2018.12.003), which describes the localisation ontology with example images and comparison to Leishmania.

Sagittal section images showing cross-section of the stomodeal valve at point of greatest opening of 15 sand flies (Lutzomyia longipalpis) at various stages of infection with Leishmania mexicana. The images show the effects of an infection and of a second blood meal on the morphology of the foregut and midgut (especially thoracic midgut) compared to uninfected, control flies. Three flies were imaged by micro-CT scan in each of five groups: T7CON flies were 7 days after a non-infected blood meal. T9INF and T12INF flies were 9 and 12 days, respectively, after an infected blood meal. T6INF+ and T9INF+ flies were 6 and 9 days, respectively after an infected bloodmeal and 1 and 4 days, respectively, after a second, non-infected blood meal. The data are discussed in a paper published on 27th August 2021 in PLoS NTDs, which is accessible through the following link: https://doi.org/10.1371/journal.pntd.0009682

TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen Trypanosoma brucei by endogenous tagging with mNeonGreen (mNG). This deposition includes the localisations, ontology and microscopy data used to build the TrypTag database. Data can also be browsed at TrypTag.org. If you use this data resource please cite Billington et al. 2023 Nature Microbiology (doi:10.1038/s41564-022-01295-6). We recommend including this citation in the results or methods if TrypTag was used as part of a discovery process. If directly using TrypTag images, please also indicate in the figure legend or similar which images are from TrypTag. If carrying out a large-scale data analysis, please also cite this BioStudies deposition. Data can be mined via the cellular localization imaging or cellular component GO term searches at the genome database TriTrypDB.org (part of VEuPathDB). If you do, please also cite the genome database. You may also find the following papers informative: Dean et al. 2016 Trends in Parasitology (doi:10.1016/j.pt.2016.10.009), which describes the original project aims and workflow. Halliday et al. 2019 Molecular and Biochemical Parasitology (doi:10.1016/j.molbiopara.2018.12.003), which describes the localisation ontology with example images and comparison to Leishmania.

Sagittal section images showing cross-section of the stomodeal valve at point of greatest opening of 15 sand flies (Lutzomyia longipalpis) at various stages of infection with Leishmania mexicana. The images show the effects of an infection and of a second blood meal on the morphology of the foregut and midgut (especially thoracic midgut) compared to uninfected, control flies. Three flies were imaged by micro-CT scan in each of five groups: T7CON flies were 7 days after a non-infected blood meal. T9INF and T12INF flies were 9 and 12 days, respectively, after an infected blood meal. T6INF+ and T9INF+ flies were 6 and 9 days, respectively after an infected bloodmeal and 1 and 4 days, respectively, after a second, non-infected blood meal. The data are discussed in a paper published on 27th August 2021 in PLoS NTDs, which is accessible through the following link: https://doi.org/10.1371/journal.pntd.0009682

Female fertility depends on a finite pool of oocytes that depletes during aging, yet the spatiotemporal dynamics of this depletion remain poorly understood. Traditional methods obscure the 3D-architecture of the ovary, limiting quantitative insights. Here, we combine light-sheet microscopy, artificial intelligence (AI)-driven segmentation, and mathematical modeling to map over 85,000 oocytes in whole-ovaries across the reproductive lifespan in mouse. We find that newly-activated oocytes represent a fixed fraction of total oocyte pool despite an age-related decline in oocyte numbers. Spatial analysis revealed that oocytes are enriched along the lateral ovarian axis, and local oocyte density positively correlates with activation. We also uncover a bimodal distribution of oocyte sizes, suggesting a bottleneck during oogenesis. Finally, a differential equation-based model captures the kinetics of oocyte activation and loss. Our findings establish a quantitative framework for understanding ovarian aging and suggest that an organ-scale regulatory mechanism coordinates the age-related decline in oocyte numbers.

Macroscopic imaging and morphological assessment of mouse placentas at E9.5. Images are collected and analyzed to detect visible placental defects and developmental abnormalities.

Purpose: Retinal ganglion cell (RGC) loss in glaucoma occurs in a large fraction of patients even after intraocular pressure (IOP) is reduced. Mitochondrial dysfunction is a key mechanism that links elevated IOP to RGC degeneration. We tested whether HDAP2, a novel high-density aromatic peptide that binds cardiolipin to stabilize mitochondrial membranes, can protect RGCs in the DBA/2J mouse model. Methods: DBA/2J mice received HDAP2 (3 mg/kg, intraperitoneally, every other day) starting at 4 months of age for 8 months. IOP was measured each month to track pressure exposure. RGC survival was assessed by counting RBPMS-stained cells in retinal wholemounts and optic nerve axons in semithin toludine blue-stained sections. Results: HDAP2-treated retinas had ~49% more RGCs than untreated retinas at similar pressure exposures (p = 0.0063; F(2,59) = 5.524). At mild IOP exposure, HDAP2 preserved 58% more RGCs compared with untreated retinas, and at high IOPs, RGC survival was 180% greater. Kaplan–Meier analysis indicated that HDAP2 increased the threshold for severe RGC loss by 29 mmHg and reduced the chance of developing severe RGC degeneration by a factor of 4.6. Optic nerve axons from treated retinas were also well preserved, with axon morphologies appearing indistinguishable from controls. Axon size distributions did not change significantly among the treatment groups, suggesting that protection by HDAP2 was similar among RGC subtypes. Conclusions: HDAP2 preserved both RGCs and axons in a pressure-dependent manner and increased tolerance to IOP. These results suggest that HDAP2 may complement pressure-lowering therapy, including for normal-tension and treatment-refractory glaucoma.

We provide a dataset of 11 whole-slide images of pancreatic cross-sections of non-obese diabetic (NOD) mice that were stained for CD11c (for myeloid cells), CD3 (for T-cells), DAPI (for nuclei), F4/80 (for macrophages), glucagon (for α-cells), insulin (for β-cells), and IL-1β. We performed 7 color multispectral imaging using the Akoya Biosciences Vectra Polaris instrument under 20X magnification and a pixel size of 0.5 μm/px. We also provide clinical data including the age of surgery, highest blood glucose recording, number of intact islets in the cross section, and the range of insulitis degrees (T-/β-cell count ratios - calculated for each islet).

Transmission electron microscopy (TEM) images of pancreatic islets from male C57BL/6J mice, acquired to examine pancreatic beta-cell morphology and insulin secretory granules in a study of diet-induced obesity and weight cycling. Images are organised by animal (21181R, 21184, 21185, 21188). The dataset is associated with Winn et al., Diabetes 2022 (PMID 35802127; DOI 10.2337/db22-0161).

Microscopy image dataset of ANX A5 in cholestasis