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Cai, B.

Publications and source records attributed to Cai, B..

At least 19 recordsLinked to original sources

Causal event structure shapes convergent reactivation signatures in human cortex and language model

Humans adapt to changing environments by understanding the latent causal structure of events, and modern large language models (LLMs) increasingly exhibit analogous abilities. However, elucidating how causal knowledge is represented and integrated in the human brain and in LLMs poses a substantial challenge for cognitive science. To address this, we combine topological analysis of representational manifolds with neuroscientific analyses of reactivation. We find that event-level causal relations modulate temporally structured neural reactivation in the human brain, particularly in the angular gyrus, precuneus and prefrontal cortex. By contrast, LLMs express these relations through positionally structured representational reactivation. Despite these differences, the resulting reactivation patterns exhibit similar intrinsic manifold structure across the two systems. Together, these findings suggest that the human brain and LLM share a common principle for organizing causal knowledge.

neuroscience↗

A Practice on Antibody Hydrophobic Interaction Chromatography Retention Time Prediction using Pre-Trained Large Language Model Fine-Tuning

Hydrophobicity is a critical property associated with the risk of non-specific binding, and it is commonly assessed using hydrophobic interaction chromatography retention time. Several computational approaches have been developed to predict antibody developability based on pre-trained language models. Such models can be fine-tuned with limited labeled antibody sequences and, in principle, do not require structural information, which is often challenging to obtain. Nevertheless, few studies have achieved strong performance in hydrophobicity prediction without incorporating structural features. Here, we present a case study of fine-tuning the pre-trained model IgBert to predict antibody hydrophobicity. Using Herceptin as a reference, we performed hydrophobic interaction chromatography retention time experiments and generated Herceptin-adjusted datasets. The fine-tuned model achieved a best R2 of 0.916, underscoring the critical role of rigorous data quality control. We also synthesized and validated 20 commercially available antibody sequences, and the results showed that the predicted hydrophobic properties were correctly reflected. Our findings provide practical guidance and highlight considerations for future applications of fine-tuned pre-trained language models in antibody hydrophobicity prediction.

bioinformatics↗

A fast 2C-induction method reveals a barrier role of SP2 for totipotency

The acquisition of totipotency in vitro remains a major challenge, limiting our understanding of early embryogenesis and its clinical and translational applications. Here, we reported a robust and rapid chemical reprogramming system that converts mouse embryonic stem cells (mESCs) into totipotent-like cells (TLCs) within 36 hours, with efficiencies exceeding 70%. The induced cells exhibit transcriptomic, epigenomic, and functional features closely resembling 2-cell (2C) stage embryos, as confirmed by scRNA-seq, ATAC-seq, and chimeric embryo analyses. Single-cell trajectory construction revealed a branching reprogramming process that yields both successful totipotent-like and alternative, non-reprogrammed fates. Mechanistically, we identified the transcription factor SP2 as a barrier to totipotency acquisition, promoting lineage-specific gene expression while repressing totipotency networks. Collectively, our study has established a highly efficient in vitro model for totipotency induction and highlighted molecular barriers shaping cell fate decisions, providing a platform to dissect the mechanisms governing the pluripotency-to-totipotency transition.

developmental biology↗

Structure of the mammalian ciliary transition zone microtubule doublet

The ciliary transition zone gates bidirectional protein trafficking to maintain the specialized ciliary proteome using microtubule doublets as a scaffold. While ciliary axonemal doublets are well-characterized, the molecular architecture of the transition zone doublet remains elusive. Here, we report the structure of the mammalian transition zone doublet from bovine tracheal cilia using cryo-electron tomography at 4.7-5.0 [A] resolution. The transition zone doublet is a structurally independent segment defined by an 8 nm-periodic arrangement of unique microtubule-inner proteins (MIPs) and microtubule-associated proteins (MAPs). We identify the calcium-binding protein CAPSL as a lumenal MIP that forms a pseudo-helical spiral and stabilizes microtubules in vitro. Furthermore, a dense MAP network on the A-microtubule surface clashes with intraflagellar transport (IFT) motor binding sites, suggesting anterograde IFT is directed to the B-microtubule for potential regulation by MAP9. Our work provides a structural framework for understanding gated ciliary transport and transition zone-linked human ciliopathies.

Cell Biology↗

Lesion-Level-Dependent Neuroendocrine Surge Precedes Neuroinflammation and Endoplasmic Reticulum Stress in the Hypothalamus After Spinal Cord Injury: Dual-Cohort Transcriptomic Evidence for a Temporally Ordered AVP Cascade

BackgroundSpinal cord injury (SCI) triggers remote pathological changes in supraspinal regions, including neuroendocrine dysfunction that manifests clinically as hyponatremia and central diabetes insipidus. Clinical observations of lesion-level dependency and sequential transformation between these disorders suggest a temporally ordered hypothalamic cascade in which a compensatory arginine vasopressin (AVP)-driven neuroendocrine surge may precede a later neuroinflammation and endoplasmic reticulum (ER) stress-mediated neuronal exhaustion. Direct transcriptomic evidence for the temporal ordering of these events, however, has been lacking. MethodsWe performed a dual-cohort transcriptomic analysis. A discovery cohort (NCBI Sequence Read Archive PRJNA953752) comprised hypothalamic tissue from adult male Sprague-Dawley rats subjected to high-thoracic (T3) SCI, low-thoracic (T10) SCI, or sham surgery, sampled at post-injury day 7 and analyzed with edgeR/DESeq2 (|log2FC| > 1, Padj < 0.05). An independent chronic-phase validation cohort (Gene Expression Omnibus GSE297887) of hippocampal tissue from SCI and sham mice was interrogated as a sensitive supraspinal proxy for remote neuroinflammatory and ER-stress signatures. Pre-defined gene panels covered neuroendocrine, neuroinflammation, and ER-stress/unfolded-protein-response categories. ResultsIn the discovery cohort, high-thoracic SCI produced a lesion-level-dependent neuroendocrine surge in the hypothalamus: Avp (fold change 7.23; Padj = 0.002), Oxt (fold change 14.25; Padj = 2.3 x 10-7), and Ucn3 (fold change 9.22; Padj = 0.002) were among the most significantly upregulated genes genome-wide, whereas low-thoracic SCI failed to reach significance for any of these targets. Classical neuroinflammation markers and canonical ER-stress effectors remained transcriptionally silent (all Padj > 0.69). The PERK-pathway sentinel genes Trib3 and Ppp1r15a/GADD34 exhibited coordinated sub-threshold trends indicative of early activation, and Avp expression was tightly correlated with Mmp9 (r = 0.833; P = 0.0004). In the chronic-phase validation cohort, microglial P2ry12 and ferroptosis signatures were significantly upregulated (P2ry12 fold change 1.33; P = 0.008) suggesting a primed microglial state, while ER-stress effectors remained silent. ConclusionsThese data support a temporally ordered hypothalamic cascade after SCI in which an early compensatory neuroendocrine surge precedes -- and may precipitate, through biosynthetic overload and blood-brain-barrier disruption -- a subsequent neuroinflammation and ER-stress crisis. The defined molecular window between neuroendocrine activation and inflammatory/ER-stress engagement identifies a candidate therapeutic window for early neuroprotective intervention in acute SCI.

neuroscience↗

EthoClaw: An Integrated AI Workflow Platform for Automated Analysis in Neuroethology

Computational methods have advanced the analysis of animal behavior, yet significant challenges remain in data standardization, analytical reproducibility, and workflow integration. Existing computational solutions often demand extensive programming proficiency or compel users to navigate a highly fragmented ecosystem of disconnected tools for tracking, statistical analysis, and visualization. Here, we present EthoClaw, an open-source, artificial intelligence-driven workflow platform built upon the OpenClaw agentic framework, functioning as a locally deployable AI assistant for behavioral research. EthoClaw provides an integrated computational infrastructure that seamlessly bridges the gap between raw behavioral video acquisitions and publishable scientific results. In this study, we demonstrate the platforms capacity to natively ingest video data via a dual-mode tracking architecture: utilizing ultra-fast image processing for rapid object detection, and leveraging the SuperAnimal methods for precise, markerless postural tracking. To ensure maximal interoperability, EthoClaw automatically converts various tracking data formats into DeepLabCut-compatible formats, enabling high-throughput phenotyping by generating publication-quality visualizations alongside rigorous multidimensional statistical profiling. Furthermore, the platform incorporates a large language model (LLM)-driven reporting module that dynamically synthesizes analytical documents, ensuring methodological transparency. Through an open field test, we validate the practical usability of EthoClaw while accelerating computational throughput by localizing heavy video processing to circumvent cloud bandwidth bottlenecks. Operating via an omnichannel natural language interface that integrates seamlessly with ubiquitous instant messaging software, EthoClaw democratizes advanced computational behavioral analysis, offering a holistic, highly efficient ecosystem that enforces experimental reproducibility and open science principles.

animal behavior and cognition↗

Subcellular transcriptome sequencing with single cell APEX-seq identifies regulators of cell-cell interactions

Single-cell RNA sequencing has transformed our understanding of tissue complexity and heterogeneous cell states, yet provides little information about the subcellular organization of transcriptomes - despite the central role of RNA localization in splicing, translation, and function. Here we introduce single-cell APEX-seq (scAPEX-seq), a proximity labeling-based method for mapping subcellular transcriptomes at single-cell resolution. Improvements in probe design and RNA recovery enable APEX integration with droplet-based RNA-seq to capture endoplasmic reticulum-associated transcripts from thousands of individual cells. Applied to tumor-macrophage co-cultures, ER-targeted scAPEX-seq revealed interaction-dependent cell states and transcriptomic signatures by enriching for cell surface and secretory transcripts that are poorly resolved by conventional scRNA-seq. We further applied scAPEX-seq to short- and long-term co-cultures of HER2+ tumor cells with human chimeric antigen receptor (CAR) T cells, resolving distinct activated CAR T cell states, including populations characterized by upregulated NT5E or CTSW expression. We showed that overexpression of CTSW, a cathepsin protease, in CAR T cells promotes stem-like phenotypes, long-term proliferation, and sustained tumor cell killing. scAPEX-seq provides a powerful and scalable approach for profiling subcellular RNA populations, enabling the discovery of cell-cell interaction regulators missed by conventional approaches.

cell biology↗

Functional impact of PCSK9 variants on LDL uptake in a knockout hepatic model

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a central regulator of low-density lipoprotein (LDL) cholesterol metabolism, yet the functional consequences of many clinically observed PCSK9 variants remain unknown. To establish a rigorous system for quantitative variant assessment, we generated a PCSK9 knockout (KO) HepG2 cell line through CRISPR/Cas9-mediated deletion of exons 2-8, effectively removing both the prodomain and catalytic regions required for PCSK9 function. This null background enabled systematic functional mapping of wild-type (WT) PCSK9 and multiple clinically relevant variants representing well-characterized, recurrent, and previously understudied alleles. Functional assays revealed pronounced heterogeneity among variant activities. The classical gain-of-function (GOF) variants D374Y and R496W exhibited robust suppression of LDL uptake, whereas A443T--an infrequently reported and previously uncharacterized variant--demonstrated a loss-of-function (LOF)-like phenotype with significantly enhanced LDL uptake. Additional poorly characterized variants, including V4I, R104C/V114A, and R496W/N425S, displayed minimal functional profiles, providing novel mechanistic insights. Surface LDL receptor (LDLR) levels generally correlated with LDL uptake but revealed unique patterns for specific variants. This KO-based rescue system provides a high-resolution framework for mechanistic classification of both established and poorly characterized PCSK9 variants, bridging the gap between genetic discovery and functional interpretation while supporting precision lipid-lowering strategies.

biochemistry↗

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

Using a GPT-5-driven autonomous lab to optimize the cost and titer of cell-free protein synthesis

We used an autonomous lab, comprising a large language model (LLM) and a fully automated cloud laboratory, to optimize the cost efficiency of cell-free protein synthesis (CFPS). By conducting iterative optimization, the LLM-driven autonomous lab was able to achieve a 40% reduction in the specific cost ($/g protein) of CFPS relative to the state of the art (SOTA). This cost reduction was accompanied by a 27% increase in protein production titer (g/L). Iterative experimental design, experiment execution, data capture and analysis, data interpretation, and new hypothesis generation were all handled by the LLM-driven autonomous lab. The interface between OpenAIs GPT-5 LLM and Ginkgo Bioworks cloud laboratory incorporated built-in validation checks via a Pydantic schema to ensure that AI-designed experiments were properly specified. Experimental designs were translated into programmatic specification of multi-instrument biological workflows by Ginkgos Catalyst software and executed on Ginkgos Reconfigurable Automation Cart (RAC) laboratory automation platform, with human intervention largely limited to reagent and consumables preparation, loading and unloading. By integrating LLMs with programmatic control of a cloud lab, we demonstrate that an LLM-driven autonomous lab can successfully perform a real-world scientific task, highlighting the potential of AI-driven autonomous labs for scientific advancement.

synthetic biology↗

Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis

BackgroundMacrophages are key players in the pathogenesis of atherosclerosis. They trigger immune responses through their cell-surface receptors. However, how macrophages regulate those receptors in response to pro-inflammatory stimuli is not completely understood. Endocytic membrane trafficking involving receptor internalization, followed by endosomal transport and recycling of the internalized receptors, plays essential roles in balancing cell-surface receptors to meet cellular needs. Here, we explored the role of the endocytic regulator EHD1 in immune responses in macrophages and determined its contribution to atherosclerosis progression. MethodsEHD1 expression profiles in mouse and human plaques were determined by single-cell RNA sequencing (scRNA-seq) and immunofluorescence staining. Bone marrow transplantation (BMT) by transplanting bone marrow cells from Ehd1-/- or littermate wild-type mice to irradiated Ldlr-/- mice was performed to determine the effect of EHD1 deletion on atherosclerosis progression. In vitro mechanistic studies including inflammation signaling and endocytosis assays were performed in bone marrow-derived macrophages. ResultsEHD1 expression in macrophages is enhanced as atherosclerosis progresses in both mice and humans. Histological analysis of aortic root sections from BMT mice showed that EHD1 deletion reduces lesion size. ScRNA-seq of aortic CD45+ cells demonstrated that EHD1 deletion attenuates pro-inflammatory responses and cell-cell interactions. Mechanistic studies revealed that EHD1 accelerates the endocytic recycling of TNFR2 and activates NF-kB, leading to increased expression of inflammatory cytokines. Moreover, EHD1 interacts with retromer and stabilizes sortilin, a retrograde cargo of retromer and a risk factor for atherosclerosis. ConclusionsEHD1 promotes inflammation by enhancing TNFR2-NF-kB signaling and stabilizing sortilin, leading to accelerated atherosclerosis. Our study reveals novel roles for EHD1-mediated membrane trafficking in macrophage function and paves the way to innovative therapeutic strategies that aim to address dysregulated membrane trafficking in atherosclerosis.

cell biology↗

Optic nerve regeneration requires the intracellular domain of LIFRa/CD118

Identifying cell-autonomous and non-autonomous factors that govern retinal ganglion cells (RGCs) ability to extend axons is an important step in developing therapies to achieve recovery after optic nerve injury. Here we report that the intracellular domain of the leukemia inhibitory factor receptor (LIFR/CD118) is essential for mature RGCs ability to regenerate injured axons independent of the cognate ligand (LIF) and other therapies. Overexpression of LIFR in adult RGCs induces neurite outgrowth in cultured RGCs and axon regeneration in vivo while strongly amplifying RGCs response to LIF itself and to unrelated growth factors. Conversely, in loss-of-function studies, down-regulation of LIFR eliminates the pro-regenerative effects of Pten deletion and other potent stimuli. LIFR bidirectionally regulates the constitutive activity of the MAP kinase pathway, in contrast to LIF itself, which primarily activates pSTAT3. Expression of a truncated LIFR lacking the extracellular domain is sufficient to promote axon regeneration and selectively increases the survival of particular RGC subtypes, placing the LIFR intracellular domain as an essential, cell-autonomous regulator of optic nerve regeneration.

neuroscience↗

The DDIT4L-TOM40-ATP5A pathway suppresses glioblastoma oncogenesis

The characteristics of glioblastoma (GBM), including resistance to cell death and aberrant energy metabolism, are associated with the function of mitochondria. To date, the inherent suppressors that couple mitochondrial function with cell death remain unclear. DNA damage-inducible transcript 4-like (DDIT4L) expression in human gliomas and its association with patient survival was determined by public databases, western-blot and immunostaining. The role of DDIT4L in regulating tumor growth was analyzed using lentivirus and PDX model. The mechanism of DDIT4L on GBM mitochondrial function was determined by different assays. Here, we show that DDIT4L is an endogenous inhibitor of GBM via suppressing mitochondrial function. DDIT4L was expressed at high levels in GBM and transported into mitochondria via single import channel TOM40 other than the import receptors TOM22, TOM20 or TOM70. Then, DDIT4L interacted with the subunit of ATP synthase, inhibited mitochondrial function and induced tumor cell apoptosis. Furthermore, the synthetic peptide DDIT4LV125-P132 suppressed GBM oncogenesis. Based on these results, DDIT4L suppresses GBM oncogenesis through both TOM40- and ATP5A-dependent mechanisms to curb mitochondrial dynamics and induce cell apoptosis, and the DDIT4LV125-P132 peptide is a potential therapy for GBM.

cancer biology↗

The HORMA-domain protein ASY1 recruits the plant-specific cyclin SDS to promote DMC1-mediated meiotic recombination

The chromosome axis is a proteinaceous scaffold essential for crossover formation in meiosis. While the axis associated HORMA-domain protein ASY1 is known to be necessary for the localization of the recombinase DMC1 to the axis, the molecular mechanism linking ASY1 to DMC1 loading remains unclear. Here, we demonstrate that ASY1 directly recruits the plant-specific cyclin SDS to chromosomes, which ensures efficient DMC1 localization and interhomolog recombination. Live-cell imaging and immunodetection revealed that SDS localizes to chromosomes from leptotene to zygotene and dissociates from chromosomes after pachytene resembling DMC1 dynamics. Biochemical assays demonstrated a direct interaction between ASY1 and SDS. Further analyses revealed that ASY1s closure motif, a conformational regulatory element, is required for SDS recruitment despite being dispensable for ASY1s own chromosome association. Moreover, unlike in sds mutants, depletion of the DMC1 inhibitor FIGL1-FLIP complex failed to restore DMC1 foci in asy1 mutants, positioning ASY1 upstream of both positive (SDS) and negative (FIGL1-FLIP) regulators of DMC1. These findings establish ASY1 as a key coordinator of meiotic recombination, bridging chromosome axis architecture with recombinase dynamics to control crossover formation and genome stability.

plant biology↗

Reinforcement of Fibrillar Collagen Hydrogels with Bioorthogonal Covalent Crosslinks

Bioorthogonal covalent crosslinking stabilizes collagen type I hydrogels, improving their structural integrity for tissue engineering applications with encapsulated living cells. The chemical modification required for crosslinking, however, interferes with the fibrillar nature of the collagen, leading instead to an amorphous network without fibers. We demonstrate an approach to perform bioconjugation chemistry on collagen with controlled localization such that the modified collagen retains its ability to self-assemble into a fibrillar network, while also displaying functional groups for covalent crosslinking with bioorthogonal click chemistry. The collagen matrix is formed through a sequential crosslinking process, in which the modified collagen first physically assembles into fibers and then is covalently crosslinked. This approach preserves the fibrous architecture of the collagen, guiding the behavior of encapsulated human corneal mesenchymal stromal cells, while also reinforcing fibers through covalent crosslinks, strengthening the stability of the cell-laden collagen hydrogel against cell-induced contraction and enzymatic degradation.

bioengineering↗

In Situ UNIversal Orthogonal Network (UNION) Bioink Deposition for Direct Delivery of Corneal Stromal Stem Cells to Corneal Wounds

The scarcity of human donor corneal graft tissue worldwide available for corneal transplantation necessitates the development of alternative therapeutic strategies for treating patients with corneal blindness. Corneal stromal stem cells (CSSCs) have the potential to address this global shortage by allowing a single donor cornea to treat multiple patients. To directly deliver CSSCs to corneal defects within an engineered biomatrix, we developed a UNIversal Orthogonal Network (UNION) collagen bioink that crosslinks in situ with a bioorthogonal, covalent chemistry. This cell-gel therapy is optically transparent, stable against contraction forces exerted by CSSCs, and permissive to the efficient growth of corneal epithelial cells. Furthermore, CSSCs remain viable within the UNION collagen gel precursor solution under standard storage and transportation conditions. This approach promoted corneal transparency and re-epithelialization in a rabbit anterior lamellar keratoplasty model, indicating that the UNION collagen bioink serves effectively as an in situ-forming, suture-free therapy for delivering CSSCs to corneal wounds. TEASER. Corneal stem cells are delivered within chemically crosslinked collagen as a transparent, regenerative biomaterial therapy.

bioengineering↗

Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability

Hydrogels composed of collagen, the most abundant protein in the human body, are widely used as scaffolds for tissue engineering due to their ability to support cellular activity. However, collagen hydrogels with encapsulated cells often experience bulk contraction due to cell-generated forces, and conventional strategies to mitigate this undesired deformation often compromise either the fibrillar microstructure or cytocompatibility of the collagen. To support the spreading of encapsulated cells while preserving the structural integrity of the gels, we present an interpenetrating network (IPN) of two distinct collagen networks with different crosslinking mechanisms and microstructures. First, a physically self-assembled collagen network preserves the fibrillar microstructure and enables the spreading of encapsulated human corneal mesenchymal stromal cells. Second, an amorphous collagen network covalently crosslinked with bioorthogonal chemistry fills the voids between fibrils and stabilizes the gel against cell-induced contraction. This collagen IPN balances the biofunctionality of natural collagen with the stability of covalently crosslinked, engineered polymers. Taken together, these data represent a new avenue for maintaining both the fiber-induced spreading of cells and the structural integrity of collagen hydrogels by leveraging an IPN of fibrillar and amorphous collagen networks. Statement of significanceCollagen hydrogels are widely used as scaffolds for tissue engineering due to their support of cellular activity. However, collagen hydrogels often undergo undesired changes in size and shape due to cell-generated forces, and conventional strategies to mitigate this deformation typically compromise either the fibrillar microstructure or cytocompatibility of the collagen. In this study, we introduce an innovative interpenetrating network (IPN) that combines physically self-assembled, fibrillar collagen--ideal for promoting cell adhesion and spreading--with covalently crosslinked, amorphous collagen--ideal for enhancing bulk hydrogel stability. Our IPN design maintains the native fibrillar structure of collagen while significantly improving resistance against cell-induced contraction, providing a promising solution to enhance the performance and reliability of collagen hydrogels for tissue engineering applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/612534v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@80cd61org.highwire.dtl.DTLVardef@2bc8aborg.highwire.dtl.DTLVardef@838c15org.highwire.dtl.DTLVardef@61dceb_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

MitoStructSeg: A Comprehensive Platform for Mitochondrial Structure Segmentation and Analysis

Mitochondrial morphology and structural changes are closely associated with metabolic dysfunction and disease progression. However, the structural complexity of mitochondria presents a major challenge for accurate segmentation and analysis. Most existing methods focus on delineating entire mitochondria but lack the capability to resolve fine internal features, particularly cristae. In this study, we introduce MitoStructSeg, a deep learning-based framework for mitochondrial structure segmentation and quantitative analysis. The core of MitoStructSeg is AMM-Seg, a novel model that integrates domain adaptation to improve cross-sample generalization, dual-channel feature fusion to enhance structural detail extraction, and continuity learning to preserve spatial coherence. This architecture enables accurate segmentation of both mitochondrial membranes and intricately folded cristae. MitoStructSeg further incorporates a quantitative analysis module that extracts key morphological metrics, including surface area, volume, and cristae density, allowing comprehensive and scalable assessment of mitochondrial morphology. The effectiveness of our approach has been validated on both human myocardial tissue and mouse kidney tissue, demonstrating its robustness in accurately segmenting mitochondria with diverse morphologies. In addition, we provide an open source, user-friendly tool to ensure practical usability.

bioinformatics↗