Cellular & Molecular Imaging
Light/fluorescence microscopy of cells & tissues, and electron/cryo-EM imaging of macromolecular structures — a metadata catalog with a durable link back to the source archive, not a hosted image gallery. These are primary research datasets (often multi-GB to multi-TB), so this platform never downloads or stores the underlying imaging data itself. Datasets already in either source archive are ingested via accession paste/CSV at /mirroring by a Continental Admin (no automated harvesting — neither source archive supports geography-filterable search); a dataset not yet in either archive can instead be submitted directly below by any node operator, for Continental Admin review. Either way, whoever submits an accession or a self-submitted dataset is the one asserting African origin — this platform does not verify it.
curl "https://<hub-domain>/api/v1/cellular-imaging"
Darwin Tree of Life - NHM samples image catalogue
BioImage Archive:S-BIAD588 · Inez Januszczak (Natural History Museum, London) · Adansonia digitata
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).
publicrestrictedAFDSI-CELL-1Integrative Chemical Genetics Platform Identifies Condensate Modulators Linked to Neurological Disorders
BioImage Archive:S-BIAD3024 · (Yale University) · Eragrostis tef
Aberrant biomolecular condensates are implicated in multiple incurable neurological disorders, including Amyotrophic Lateral Sclerosis, Frontotemporal Dementia, and DYT1 dystonia. However, the role of condensates in driving disease etiology remains incompletely understood. Here, we establish myeloid leukemia factor 2 (MLF2) as a disease-associated phase transition biomarker and develop a scalable high-content platform that identifies condensate modulators across broad chemical and genetic space. We uncover FDA-approved drugs that remodel aberrant condensate composition, validating the approach for drug discovery. A genome-wide CRISPR/Cas9 screen identifies genes linked to microcephaly and related neurodevelopmental disorders whose loss drives nuclear condensate accumulation. Machine learning resolves two phenotypic clusters: RNF26 deletion induces nuclear envelope condensates reminiscent of nuclear pore defects, whereas loss of microcephaly-associated ZNF335 drives accumulation of distinct nucleoplasmic condensates. Our study provides a scalable resource for identifying corrective modulators of aberrant condensates and establishes a link between dysregulated phase transitions and neurodevelopmental disorders.
publicrestrictedAFDSI-CELL-2Darwin Tree of Life - NHM samples image catalogue
BioImage Archive:S-BIAD588 · Inez Januszczak (Natural History Museum, London) · Gambeya albida
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).
publicrestrictedAFDSI-CELL-3The European Reference Genome Atlas - COPO submission
BioImage Archive:S-BIAD1012 · Various Sample Collectors COPO Project (Earlham Institute) · Helichrysum odoratissimum
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.
publicrestrictedAFDSI-CELL-4Darwin Tree of Life - NHM samples image catalogue
BioImage Archive:S-BIAD588 · Inez Januszczak (Natural History Museum, London) · Heterocephalus glaber
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).
publicrestrictedAFDSI-CELL-5Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment
BioImage Archive:S-BIAD1443 · Jen-Hung Wang (Technical University of Denmark) · Panthera leo
This repository presents an objective, quantifiable method for assessing atopic dermatitis (AD) severity. The program integrates deep learning object detection with spatial analysis algorithms to accurately calculate the density of circular nano-size objects (CNOs), termed the Effective Corneocyte Topographical Index (ECTI). The ECTI demonstrates remarkable robustness in overcoming the inherent challenges of nano-imaging, such as environmental noise and structural occlusions on the corneocyte surface, further enhancing its applicability in clinical settings.
publicrestrictedAFDSI-CELL-6Experimental Data for CombPlex Paper: "Escalating High-dimensional Imaging using Combinatorial Channel Multiplexing and Deep Learning"
BioImage Archive:S-BIAD873 · Leeat Keren (Weizmann Institute of Science) · Sorghum bicolor
Data for all the experiments described in our paper: "Escalating High-dimensional Imaging using Combinatorial Channel Multiplexing and Deep Learning". For further information, please refer to our paper or visit our git repository. Link to our paper: https://www.biorxiv.org/content/10.1101/2023.09.09.556962v1 Link to our GitHub repository: https://github.com/KerenLab/CombPlex
publicrestrictedAFDSI-CELL-11Darwin Tree of Life - NHM samples image catalogue
BioImage Archive:S-BIAD588 · Inez Januszczak (Natural History Museum, London) · Sorghum bicolor
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).
publicrestrictedAFDSI-CELL-12Darwin Tree of Life - NHM samples image catalogue
BioImage Archive:S-BIAD588 · Inez Januszczak (Natural History Museum, London) · Struthio camelus
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).
publicrestrictedAFDSI-CELL-13Darwin Tree of Life - NHM samples image catalogue
BioImage Archive:S-BIAD588 · Inez Januszczak (Natural History Museum, London) · Vigna unguiculata
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).
publicrestrictedAFDSI-CELL-14Polyphasic Characterization and Biotechnological Potential of Three Novel Prochlorococcaceae (Cyanobacteria) Genera: An Integrative Taxonomic Approach Combining 16S rRNA gene, Genomic and Chemotaxonomic Analyses
BioImage Archive:S-BIAD2816 · (CIIMAR) · Panthera leo
The strains LEGE 06306, LEGE 06307, LEGE 11436, and LEGE 10375, isolated from northern Portugal, were characterized using a polyphasic taxonomic approach that included 16S rRNA gene phylogenetic analyses (ML and BI), 16S-23S ITS secondary structures, p-distance calculations, phylogenomics, morphological and ultrastructural (TEM) observations, MALDI-TOF MS profiling, as well as ecological and biochemical characterization. Although LEGE 06306, LEGE 06307, and LEGE 11436 share high 16S rRNA gene sequence similarity and display very similar morphology, the three ML and BI phylogenetic analyses revealed that these strains form three distinct lineages within the family Prochlorococcaceae, without consistent affiliation to any previously described genera. The phylogenomic analysis, ITS comparisons, and the biochemical statistical comparisons further supported the separation of these lineages. MALDI-TOF analysis revealed unique spectral profiles for each strain, while their pigment compositions were similar but varied in pigment concentrations, supporting their distinction. Based on these combined results, the three strains are described as representatives of three new cyanobacterial genera. Strain LEGE 10375 showed an uncertain placement in both the 16S rRNA and whole-genome phylogenies and therefore could not be taxonomically assigned. The high content of bioactive metabolites of the studied strains, including pigments, phenolic compounds, and sugars, positions them as sustainable sources for functional ingredients with potential applications in the food, feed, and pharmaceutical industries.
publicrestrictedAFDSI-CELL-7Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation
BioImage Archive:S-BIAD2969 · (University of Copenhagen) · Panthera leo
Cell state transitions underlie the emergence of diverse cell types and are traditionally defined by changes in gene expression. Yet these transitions also involve coordinated shifts in cell morphology and behaviour, which remain poorly characterized in densely packed epithelia. We developed a quantitative live-imaging and computational framework to track thousands of individual cells over time in the rapidly differentiating Xenopus mucociliary epithelium (MCE). From segmentations and trajectories, we extracted dynamic features—cell and nuclear shape, movement, and position—to create a time-resolved morphodynamic dataset spanning the full course of differentiation. While single features showed high noise and low separability of ground-truth cell types, supervised machine learning revealed that integrating time-resolved features robustly predicts final cell fate. Gradient-boosted trees and multinomial logistic regression achieved moderate but consistent accuracy, especially for abundant epithelial lineages. Key discriminants included normalized Z position, membrane–nucleus offset, and absolute experimental time, whereas movement contributed minimally to the results. Our data show that morphodynamic signatures encode predictive information about cell identity and provide a framework linking cellular dynamics with molecular state.
publicrestrictedAFDSI-CELL-8Modular, portable, high-end microscopy inside and outside the lab
BioImage Archive:S-BIAD3530 · (BIH - Berlin Institute of Health at Charité - Universitätsmedizin Berlin) · Xenopus laevis
Advances in biological imaging have transformed our understanding of living systems, yet access to state-of-the-art microscopy remains out of reach for many researchers. This is specially true for those without direct access to specialized optics laboratories or those working with non-model organisms. To overcome these barriers, we developed Flamingo: an adaptable, modular, and portable light sheet microscope designed for diverse research environments. Flamingo enables dynamic reconfiguration to suit a wide range of imaging needs and facilitates high-quality data acquisition directly in biological labs or field stations. We utilized Flamingo to image a range of intact, living, and cleared samples, demonstrating its versatility across various sample types and experimental conditions. Our fully assembled, ready-to-use Flamingo empowers biologists to pursue novel research questions and democratizes access to advanced microscopy.
publicrestrictedAFDSI-CELL-20The increase of Cyclin A/cdk activity and of FAM122A-dependent inhibition of PP2A-B55 are key events to trigger mitosis
BioImage Archive:S-BIAD984 · Benjamin Lacroix (Université de Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France. ) · Xenopus laevis
Microscopy images and movies used for our publication "The increase of Cyclin A/cdk activity and of FAM122A-dependent inhibition of PP2A-B55 are key events to trigger mitosis"
publicrestrictedAFDSI-CELL-21The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples
BioImage Archive:S-BIAD963 · Nikita Vladimirov (University of Zurich) · Xenopus laevis
In 2015, we launched the mesoSPIM initiative (www.mesospim.org), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of light-sheet microscopy. Here, we introduce the next-generation mesoSPIM ("Benchtop") with significantly increased field of view, improved resolution, higher throughput, more affordable cost and simpler assembly compared to the original version. We developed a new method for testing objectives, enabling us to select detection objectives optimal for light-sheet imaging with large-sensor sCMOS cameras. The new mesoSPIM achieves high spatial resolution (1.5 µm laterally, 3.3 µm axially) across the entire field of view, a magnification up to 20x, and supports sample sizes ranging from sub-mm up to several centimetres, while being compatible with multiple clearing techniques. The new microscope serves a broad range of applications in neuroscience, developmental biology, and even physics.
publicrestrictedAFDSI-CELL-22BioImage Archive:S-BIAD553 · Guillermo Serrano Nájera (University of Cambridge) · Xenopus laevis
1) Light-sheet movies of the surface of chick embryos treated with different chemicals at cellular resolution. Ideal to study individual cell behaviours and tissue flows in epithelial tissues. 2) Confocal images of SNAI2 and pMLC2 of chick embryos treated with different chemicals.
Fluorescence microscopy
publicrestrictedAFDSI-CELL-23Optogenetic control of a GEF of RhoA uncovers a signaling switch from retraction to protrusion
BioImage Archive:S-BIAD1842 · Jean de seze (Institut Curie) · Panthera leo
The ability of a single protein to trigger different functions is an assumed key feature of cell signaling, yet there are very few examples demonstrating it. Here, using an optogenetic tool to control membrane localization of RhoA nucleotide exchange factors (GEFs), we present a case where the same protein can trigger both protrusion and retraction when recruited to the plasma membrane, polarizing the cell in two opposite directions. We show that the basal concentration of the GEF prior to activation predicts the resulting phenotype. A low concentration leads to retraction, whereas a high concentration triggers protrusion. This unexpected protruding behavior arises from the simultaneous activation of Cdc42 by the GEF and sequestration of active RhoA by the GEF PH domain at high concentrations. We propose a minimal model that recapitulates the phenotypic switch, and we use its predictions to control the two phenotypes within selected cells by adjusting the frequency of light pulses. Our work exemplifies a unique case of control of antagonist phenotypes by a single protein that switches its function based on its concentration or dynamics of activity. It raises numerous open questions about the link between signaling protein and function, particularly in contexts where proteins are highly overexpressed, as often observed in cancer.
publicrestrictedAFDSI-CELL-9High Content 3D Imaging by Dual-View Oblique Plane Microscopy
BioImage Archive:S-BIAD2314 · (Imperial College London, London, UK) · Panthera leo
Oblique plane microscopy (OPM) is a form of light-sheet fluorescence microscopy (LSFM) employing a single microscope objective at the sample for both fluorescence excitation and detection. Dual-view OPM (dOPM) is an optically folded form of OPM. We present an improved dOPM system employing a 60×/1.2NA water immersion primary objective and measure the spatial resolution and fluorescence collection efficiency for illumination angles of 35° and 45° with respect to the coverslip. Illumination at 35° provides slightly better lateral resolution and collection efficiency. Collection efficiency measurements are compared to a full vectorial raytracing simulation of the system. Using a light-sheet angle of 35°, the median bead FWHM for 100 nm diameter fluorescent beads in x, y and z and the optical sectioning strength were measured over a volume of 100×100×100 μm³, to be 0.29, 0.31, 0.83 and 2.45-3.00 μm respectively when the two dOPM views are fused. We demonstrate less photobleaching in time-lapse dOPM of live mEmerald-expressing organoids compared to widefield epi-fluorescence z-stack imaging under the condition of equal detected fluorescence signal from a point object in focus. We demonstrate dOPM for multi-field-of-view 3D imaging of biological samples in 96-well plates and apply it to imaging cells in collagen gel and quantifying the FUCCI cell-cycle reporter to provide drug dose-response curves in spheroids. We also use it to perform time-lapse multi-field-of-view imaging and demonstrate the detection of organoid lumen closure and reopening, organoid migration within a collagen gel and observing dynamic events in arrays of ex vivo tissue slices.
publicrestrictedAFDSI-CELL-10Phosphorylation of Xenopus M18BP1 governs centromeric localization and CENP-A nucleosome assembly (EMBO Reports)
BioImage Archive:S-BIAD2416 · (Stanford University) · Xenopus laevis
Eukaryotic chromosome segregation requires attachment of chromosomes to microtubules through the kinetochore so that chromosomes can align and move in mitosis. Kinetochores assemble on the centromere which is epigenetically defined by the histone H3 variant CENtromere Protein A (CENP-A). During DNA replication CENP-A is equally divided between replicated chromatids and new CENP-A nucleosomes are re-assembled during the subsequent G1 phase. How cells regulate the cell cycle timing of CENP-A assembly is a central question in the epigenetic maintenance of centromeres. CENP-A nucleosome assembly requires the Mis18 complex (Mis18α, Mis18β, and M18BP1) which is regulated in its localization to centromeres between metaphase and G1. Here, we define a new regulatory mechanism that works through phosphorylation of Xenopus laevis M18BP1 between metaphase and interphase. This switch disrupts binding of M18BP1 to CENP-A nucleosomes in metaphase, and when relieved enables M18BP1 binding to CENP-A nucleosomes in interphase. We show that this phosphorylation dependent mechanism regulates CENP-A nucleosome assembly. We propose that the phospho-regulated binding of M18BP1 to CENP-A nucleosomes restricts new CENP-A assembly to interphase.
publicrestrictedAFDSI-CELL-15Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension in Xenopus
BioImage Archive:S-BIAD3568 · (UAB - University of Alabama at Birmingham) · Xenopus laevis
Convergent extension (CE) is a fundamental morphogenetic process where oriented cell behaviors lead to polarized extension of diverse tissues. In vertebrates, regulation of CE requires both non-canonical Wnt, its co-receptor Ror, and several 'core members' of the planar cell polarity (PCP) pathway. PCP was originally identified as a mechanism to coordinate the cellular polarity in the plane of static epithelium, where core proteins Frizzled (Fz)/Dishevelled (Dvl) and Van Gogh-like (Vangl)/Prickle (Pk) partition to opposing cell cortex. But how core PCP proteins interact with each other to mediate non-canonical Wnt/Ror signaling during CE is not clear. We found previously that during CE, Vangl cell-autonomously recruits Dvl to the plasma membrane and keeps Dvl inactive. In this study, we show that non-canonical Wnt induces Dvl to transition from Vangl to Fz in Xenopus embryos. Pk inhibits the transition and functionally synergizes with Vangl to suppress Dvl during CE. Conversely, Ror is required for the transition and functionally antagonizes Vangl. Biochemically, Vangl interacts directly with both Ror and Dvl. Ror and Dvl do not bind directly but can be co-fractionated with Vangl. Collectively, we propose that Pk assists Vangl to function as an unconventional adaptor that brings Dvl and Ror into a complex to serve two functions: (1) simultaneously preventing both Dvl and Ror from ectopically activating non-canonical Wnt signaling; and (2) relaying Dvl to Fz for signaling activation upon non-canonical Wnt-induced dimerization of Fz and Ror.
publicrestrictedAFDSI-CELL-16Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension in Xenopus
BioImage Archive:S-BIAD3569 · (UAB - University of Alabama at Birmingham) · Xenopus laevis
Convergent extension (CE) is a fundamental morphogenetic process where oriented cell behaviors lead to polarized extension of diverse tissues. In vertebrates, regulation of CE requires both non-canonical Wnt, its co-receptor Ror, and several ‘core members’ of the planar cell polarity (PCP) pathway. PCP was originally identified as a mechanism to coordinate the cellular polarity in the plane of static epithelium, where core proteins Frizzled (Fz)/Dishevelled (Dvl) and Van Gogh-like (Vangl)/Prickle (Pk) partition to opposing cell cortex. But how core PCP proteins interact with each other to mediate non-canonical Wnt/Ror signaling during CE is not clear. We found previously that during CE, Vangl cell-autonomously recruits Dvl to the plasma membrane and keeps Dvl inactive. In this study, we show that non-canonical Wnt induces Dvl to transition from Vangl to Fz in Xenopus embryos. Pk inhibits the transition and functionally synergizes with Vangl to suppress Dvl during CE. Conversely, Ror is required for the transition and functionally antagonizes Vangl. Biochemically, Vangl interacts directly with both Ror and Dvl. Ror and Dvl do not bind directly but can be co-fractionated with Vangl. Collectively, we propose that Pk assists Vangl to function as an unconventional adaptor that brings Dvl and Ror into a complex to serve two functions: (1) simultaneously preventing both Dvl and Ror from ectopically activating non-canonical Wnt signaling; and (2) relaying Dvl to Fz for signaling activation upon non-canonical Wnt-induced dimerization of Fz and Ror.
publicrestrictedAFDSI-CELL-17Palmitoylated Importin Alpha Regulates Mitotic Spindle Orientation Through Interaction with NuMA
BioImage Archive:S-BIAD1801 · Patrick James Sutton (Stony Brook University) · Xenopus laevis
Microscopy data for manuscript: "Palmitoylated Importin Alpha Regulates Mitotic Spindle Orientation Through Interaction NuMA". A study elucidating a novel role of the nuclear transport protein importin alpha in astral microtubule anchoring.
publicrestrictedAFDSI-CELL-18Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation
BioImage Archive:S-BIAD2969 · (University of Copenhagen) · Xenopus laevis
Cell state transitions underlie the emergence of diverse cell types and are traditionally defined by changes in gene expression. Yet these transitions also involve coordinated shifts in cell morphology and behaviour, which remain poorly characterized in densely packed epithelia. We developed a quantitative live-imaging and computational framework to track thousands of individual cells over time in the rapidly differentiating Xenopus mucociliary epithelium (MCE). From segmentations and trajectories, we extracted dynamic features—cell and nuclear shape, movement, and position—to create a time-resolved morphodynamic dataset spanning the full course of differentiation. While single features showed high noise and low separability of ground-truth cell types, supervised machine learning revealed that integrating time-resolved features robustly predicts final cell fate. Gradient-boosted trees and multinomial logistic regression achieved moderate but consistent accuracy, especially for abundant epithelial lineages. Key discriminants included normalized Z position, membrane–nucleus offset, and absolute experimental time, whereas movement contributed minimally to the results. Our data show that morphodynamic signatures encode predictive information about cell identity and provide a framework linking cellular dynamics with molecular state.
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