Nature Protocols最新文献_第8页

Nonexhaustive microextraction as a step toward more sustainable chemical analysis in the field and the clinic. 非穷尽微萃取法是向野外和临床更可持续的化学分析迈出的一步。

IF 16 1区生物学

Nature Protocols Pub Date : 2026-05-28 DOI: 10.1038/s41596-026-01384-4

Wei Zhou, Janusz Pawliszyn

{"title":"Nonexhaustive microextraction as a step toward more sustainable chemical analysis in the field and the clinic.","authors":"Wei Zhou, Janusz Pawliszyn","doi":"10.1038/s41596-026-01384-4","DOIUrl":"https://doi.org/10.1038/s41596-026-01384-4","url":null,"abstract":"Advances in green analytical chemistry have resulted in the emergence of miniaturized, integrated and sustainable analytical workflows that deliver high performance with minimal environmental impact. However, conventional sample preparation remains a critical bottleneck, as it typically relies on exhaustive extraction approaches, where targeted analytes are removed from the sample material through laborious, solvent-intensive and time-consuming procedures. By contrast, many familiar analytical measurements are quantitative despite being inherently nonexhaustive: for example, pH detectors or glucose indicator strips, which interrogate a system without depleting the analyte. Sharing the same principle, nonexhaustive partitioning enrichment-exemplified by the solid-phase microextraction approach-provides an effective alternative to multicomponent determinations by integrating sampling, extraction, cleanup and enrichment within a single step. A wide variety of sorbent materials can be used to coat different objects-this combination can be optimized for the targeted analytes, sample matrix or chosen downstream detection method. Solid-phase microextraction can be coupled with techniques such as gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry for comprehensive chemical characterization or directly interfaced with advanced detection systems such as mass spectrometry and sensors. High analytical efficiency with minimal solvent consumption is further facilitated by their capacity to be integrated into automated workflows. Together, these developments provide a conceptual framework for the next generation of sustainable sample preparation methodologies, underscoring the transition of analytical chemistry toward unified, adaptive and environmentally responsible workflows.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis and guest inclusion for molecular catcher-based structure determination. 分子捕集剂结构测定的合成与客体包合。

IF 16 1区生物学

Nature Protocols Pub Date : 2026-05-27 DOI: 10.1038/s41596-026-01370-w

Yitao Wu, Lei Xu, Shang Li, Hongyan Zhang, Shiyuan Wang, Jiahao Yu, Jiyong Liu, Jonathan L Sessler, Feihe Huang

{"title":"Synthesis and guest inclusion for molecular catcher-based structure determination.","authors":"Yitao Wu, Lei Xu, Shang Li, Hongyan Zhang, Shiyuan Wang, Jiahao Yu, Jiyong Liu, Jonathan L Sessler, Feihe Huang","doi":"10.1038/s41596-026-01370-w","DOIUrl":"https://doi.org/10.1038/s41596-026-01370-w","url":null,"abstract":"Natural products and drugs containing long alkyl chains are difficult to grow in the form of single crystals. This makes it challenging, if not impossible, to determine their molecular structures through conventional single-crystal X-ray diffraction. We recently reported a 'molecular catcher' technique using a pillar[5]arene-incorporated metal-organic framework (MOF), namely a 'molecular catcher', that enables rapid and accurate determination of crystal structures for long-alkyl-chain compounds without a need to grow single crystals. In this approach, presynthesized pillar[5]arene-containing MOF crystals are soaked in a solution of the target compound. The compound is captured into the MOF crystals, which are then analyzed by X-ray diffraction, allowing the crystal structure of the guest to be determined. Here we describe detailed protocols for the synthesis of this pillar[5]arene-containing MOF and its further use in structure determinations. In brief, the MOF crystals required for this Protocol are prepared from an in-house synthesized pillar[5]arene derivative, a commercially available tetraphenyl ethylene derivative and zinc nitrate hexahydrate in N,N-dimethylformamide. The resulting crystals are washed with fresh N,N-dimethylformamide to remove unreacted starting materials and can be used directly for guest inclusion without further solvent exchange. The most critical step is selecting MOF crystals with suitable size and quality. We recommend using optical microscopy for preliminary screening to evaluate crystal size and quality as the selection criteria. By soaking the MOF crystals in a solution of the target compound, target-included MOF crystals suitable for X-ray diffraction analysis can be obtained. The entire process-from starting materials to determining the crystal structure-can be completed within 10 d.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148043067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A generic, rapid and robust platform for personalized functional circuit-guided neuromodulation targeting. 一个通用，快速和强大的平台，个性化功能电路引导神经调节靶向。

IF 16 1区生物学

Nature Protocols Pub Date : 2026-05-27 DOI: 10.1038/s41596-026-01371-9

Wei Zhang, Shenshen Li, Ning An, Jianting Huang, Feng Wang, Danhong Wang, Yuanxiang Lin, Hesheng Liu, Jianxun Ren

{"title":"A generic, rapid and robust platform for personalized functional circuit-guided neuromodulation targeting.","authors":"Wei Zhang, Shenshen Li, Ning An, Jianting Huang, Feng Wang, Danhong Wang, Yuanxiang Lin, Hesheng Liu, Jianxun Ren","doi":"10.1038/s41596-026-01371-9","DOIUrl":"https://doi.org/10.1038/s41596-026-01371-9","url":null,"abstract":"Neuromodulation approaches can target specific brain functional circuits to treat various brain disorders, and resting-state functional magnetic resonance imaging is increasingly being used to map functional circuits in individual patients for target localization. However, this strategy faces three major hurdles for clinical translation: time-intensive resting-state functional magnetic resonance imaging processing, insufficient robustness for clinical use and a lack of automated targeting solutions. Here we cover the use of a generic, rapid, robust and automated platform for personalized functional circuit-guided target planning across different neuromodulation techniques, termed Unified Platform for Neuromodulation with Individualized Target Estimation (UNITE). UNITE is computationally efficiency and robust and uses DeepPrep, a recently developed end-to-end preprocessing pipeline that achieves a tenfold speedup and improved robustness compared with state-of-the-art clinical pipeline. Using DeepPrep's preprocessed data, UNITE maps functional circuits and localizes personalized targets through automated targeting algorithms. Currently, UNITE offers three built-in transcranial magnetic stimulation-targeting algorithms for post-stroke functional rehabilitation and one focused ultrasound stimulation-targeting algorithm for Parkinson's disease. Notably, it is designed to be adapted for other brain disorders and neuromodulation applications. To ensure quality and usability, UNITE generates a data quality control report and a visual verification report of the identified targets, with target coordinates exported in multiple formats for compatibility with different neuronavigation systems. Overall, this platform enables personalized neuromodulation target localization within 30 min on a local graphics processing unit-equipped workstation. A basic level of computer science proficiency, along with neuroimaging experience, is sufficient for its use.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148043113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeted single-cell RNA and perturbation sequencing with TAP-seq. 靶向单细胞RNA和TAP-seq微扰测序。

IF 16 1区生物学

Nature Protocols Pub Date : 2026-05-26 DOI: 10.1038/s41596-026-01367-5

Dewi P I Moonen, Daniel Schraivogel, Andreas R Gschwind, Lars M Steinmetz

{"title":"Targeted single-cell RNA and perturbation sequencing with TAP-seq.","authors":"Dewi P I Moonen, Daniel Schraivogel, Andreas R Gschwind, Lars M Steinmetz","doi":"10.1038/s41596-026-01367-5","DOIUrl":"https://doi.org/10.1038/s41596-026-01367-5","url":null,"abstract":"Pooled genome editing combined with single-cell RNA sequencing-commonly known as Perturb-seq-has transformed the ability to interrogate genome function. However, whole-transcriptome single-cell RNA sequencing requires high sequencing depth to achieve the sensitivity needed for functional genomics screens, limiting its widespread use owing to prohibitive cost. Here we describe a detailed and updated protocol for targeted Perturb-seq (TAP-seq), a method that addresses the sensitivity and cost limitations of Perturb-seq. Instead of capturing the whole transcriptome, TAP-seq focuses on quantifying hundreds of transcripts of interest. The TAP-seq workflow involves first selecting genes for targeted readout, designing primers, conducting an initial pilot experiment and finally performing the TAP-seq screen and analyzing the data. We provide comprehensive guidance on designing targeted readout strategies for TAP-seq and describe all steps of the protocol, starting with library preparation. The outcome of TAP-seq is single-cell measurements of selected gene and guide RNA expression levels, guide RNA assignments to individual cells and differential expression results revealing perturbation effects on target genes. We further include instructions for adapting TAP-seq to all currently available single-cell RNA-sequencing platforms. Prior experience in single-cell technologies is beneficial and the protocol described can be completed in 2 days (excluding data analysis). In summary, this protocol describes how to perform sensitive, scalable and cost-effective single-cell perturbation screens.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148033060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chiral multimodal nanoprobes for sensing of biomarkers 用于生物标志物传感的手性多模态纳米探针。

IF 18.4 1区生物学

Nature Protocols Pub Date : 2026-05-22 DOI: 10.1038/s41596-026-01361-x

Changlong Hao, Panpan Chen, Aihua Qu, Maozhong Sun, Liguang Xu, Chuanlai Xu, Hua Kuang

{"title":"Chiral multimodal nanoprobes for sensing of biomarkers","authors":"Changlong Hao, Panpan Chen, Aihua Qu, Maozhong Sun, Liguang Xu, Chuanlai Xu, Hua Kuang","doi":"10.1038/s41596-026-01361-x","DOIUrl":"10.1038/s41596-026-01361-x","url":null,"abstract":"Biomarker detection for early disease diagnosis demands materials with high sensitivity and anti-interference capability. However, conventional single-signal nanosensors often fail in complex biological matrices due to autofluorescence and matrix interference. Here, to address these challenges, we report the synthesis of chiral multimodal nanoprobes that integrate circular dichroism, fluorescence and magnetic resonance signals. These probes, constructed using either ‘intrinsic chiral nanomaterials’ or ‘hybrid chiral assemblies’, leverage synergistic interactions between chiral frameworks and target analytes to enable orthogonal signal cross-validation. The operation time for their synthesis is usually less than 6 h, includes rapid screening (~1 h) of sensitivity and selectivity through optimization of spectral parameters. This strategy accelerates the development of advanced sensing materials, offering a robust platform for biomarker detection in biomedical applications. The protocol requires familiarity with nanomaterial synthesis, surface functionalization and spectroscopic characterization. This protocol outlines the synthesis of chiral multimodal nanoprobes that detect biomarkers in vitro and in vivo by integrating circular dichroism, fluorescence and magnetic resonance signals.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":"21 10","pages":"4893-4925"},"PeriodicalIF":18.4,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148006179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SMAIS: a universal platform for the on-water surface synthesis of two-dimensional polymer crystals. SMAIS：一个在水面上合成二维聚合物晶体的通用平台。

IF 16 1区生物学

Nature Protocols Pub Date : 2026-05-21 DOI: 10.1038/s41596-026-01368-4

Chen Hu, Dongxu Wang, Zhiyong Wang, Xinliang Feng

{"title":"SMAIS: a universal platform for the on-water surface synthesis of two-dimensional polymer crystals.","authors":"Chen Hu, Dongxu Wang, Zhiyong Wang, Xinliang Feng","doi":"10.1038/s41596-026-01368-4","DOIUrl":"https://doi.org/10.1038/s41596-026-01368-4","url":null,"abstract":"Two-dimensional polymers (2DPs) are covalent polymeric networks with intrinsic long-range order in two orthogonal directions. Their unique physicochemical properties include tunable opto-electronic properties, mechanical stability and precisely defined nanopores that enable ion and molecular sieving. Here we describe a universal approach for the precise synthesis of 2DPs through the surfactant-monolayer-assisted interfacial synthesis method. The surfactant-monolayer-assisted interfacial synthesis combines the on-water surface reactivity and the role of surfactant (for example, sodium oleyl sulfate and sodium dodecyl benzenesulfonate) to guide the monomer-programmed assembly, two-dimensional (2D) polymerization and crystallization processes on the water surface, yielding large-area and highly crystalline 2DPs. This versatile Protocol has been used to synthesize many 2DP crystals, including 2D polyamide, 2D polyimide, 2D polyimine, 2D poly(boronate ester), 2D poly(pyridinium salt), 2D polyphenylenevinylene, 2D polybenzimidazole and 2D polyaniline, with a large lateral size of ~28 cm2. The crystals have precisely tunable thicknesses ranging from ~1 to 200 nm by adjusting the reaction time and/or reactant concentration and large crystal domain (that is, the lateral size of a single crystalline region) up to ~160 μm2, which helps minimize grain boundaries and preserve the intrinsic properties of 2DPs. Synthesis typically takes 2-14 days, depending on the reaction type. Film collection via a horizontal dipping method and a simple washing procedure, yield the target 2DPs. The resulting 2DP crystals have been integrated into electronics, optoelectronics, membranes and energy conversion/storage devices, exhibiting excellent performance. This Protocol can be performed easily by researchers with intermediate expertise in framework materials and interfacial chemistry.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147988327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Addendum: Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX 附录：基于MCScanX的共线块检测、合成和进化分析。

IF 18.4 1区生物学

Nature Protocols Pub Date : 2026-05-15 DOI: 10.1038/s41596-026-01380-8

Xi Zhang, Yupeng Wang, Paule V. Joseph, Andrew H. Paterson, David Roy Smith

引用次数: 0

Flexible high-resolution ECM micropatterning 灵活的高分辨率ECM微图。

IF 18.4 1区生物学

Nature Protocols Pub Date : 2026-05-13 DOI: 10.1038/s41596-026-01360-y

Alessandro Gandin, Veronica Torresan, Tito Panciera, Gianluca Grenci, Giada Vanni, Anna Citron, Matteo Marchionni, Giusy Battilana, Margherita Pelosin, Rebecca Busetto, Stefano Piccolo, Giovanna Brusatin

{"title":"Flexible high-resolution ECM micropatterning","authors":"Alessandro Gandin, Veronica Torresan, Tito Panciera, Gianluca Grenci, Giada Vanni, Anna Citron, Matteo Marchionni, Giusy Battilana, Margherita Pelosin, Rebecca Busetto, Stefano Piccolo, Giovanna Brusatin","doi":"10.1038/s41596-026-01360-y","DOIUrl":"10.1038/s41596-026-01360-y","url":null,"abstract":"Spatial cues and cell–cell interactions within in vivo tissue architecture generate physical signals that regulate cell behavior. These mechanical interactions drive processes such as morphogenesis, homeostasis, regeneration and disease progression. To recapitulate these spatial niches in vitro, lithographic micropatterning allows for precise control over the geometry, composition, topography and mechanics of cell-adhesive substrates. Micropatterned cultures have been essential in uncovering key mechanotransduction mechanisms, including YAP/TAZ-mediated signaling, mechanoregulation in cancer, aging and early embryonic development. However, accessible and adaptable micropatterning protocols for conventional cell biology laboratories remain limited. In this protocol, we present a comprehensive procedure for generating flexible, high-resolution micropatterns (down to 10 × 10 µm2), optimized for high-magnification confocal imaging, long-term cell culture, customizable functionalization (proteins, peptides or both) and extended shelf life. This versatile and convenient procedure can be performed by trained PhD students or postdoctoral researchers, does not require prior expertise in photolithography and can be completed within 2 d. In addition, we provide a step-by-step guide to study mechanotransduction using YAP/TAZ functional readouts that can be completed within 5 d. This protocol offers an affordable and scalable solution applicable to a wide range of biological questions, allowing for diverse experimental needs, and represents a valuable tool for advancing mechanobiology and other areas of cell biology. This protocol presents a versatile, easy-to-apply procedure for fabricating high-resolution cell-adhesive micropatterns, offering an affordable and scalable solution amenable to non-specialist cell biology teams.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":"21 10","pages":"4858-4892"},"PeriodicalIF":18.4,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fabrication of focused electron beam induced deposition tips for high-speed atomic force microscopy using benchtop scanning electron microscopy. 用台式扫描电镜制备高速原子力显微镜用聚焦电子束诱导沉积尖端。

IF 18.4 1区生物学

Nature Protocols Pub Date : 2026-05-12 DOI: 10.1038/s41596-026-01369-3

Motonori Imamura, Atsushi Miyagi, Alma P Perrino, Simon Scheuring

{"title":"Fabrication of focused electron beam induced deposition tips for high-speed atomic force microscopy using benchtop scanning electron microscopy.","authors":"Motonori Imamura, Atsushi Miyagi, Alma P Perrino, Simon Scheuring","doi":"10.1038/s41596-026-01369-3","DOIUrl":"10.1038/s41596-026-01369-3","url":null,"abstract":"High-speed atomic force microscopy (HS-AFM) movies have contributed significantly to our understanding of biomolecular dynamics, because these experiments have resolved conformational changes at submolecular resolution in aqueous environments. However, the resolution of HS-AFM images and AFM images in general critically depend on the sharpness of the tip. Focused electron beam-induced deposition (FEBID) in a scanning electron microscope (SEM) yields AFM tips with high aspect ratio and small tip radius, formed by deposition of metal-organic precursors such as ferrocene, producing amorphous carbon deposits, permissive for the reproducible acquisition of high-resolution images. Although FEBID tips are essential for HS-AFM image quality, it is common to rely on commercial cantilevers, because of limited SEM access or perceived technical barriers. Here, we showcase the use of a commercial benchtop SEM for the fabrication of FEBID tips for high-resolution AFM. To facilitate the fabrication process, we developed a cantilever and sample holder that minimize drift and mechanical vibrations during SEM operation and enable efficient and reproducible fabrication of sharp AFM tips. The shape of the FEBID tips was evaluated as a function of beam defocus, deposition time, acceleration voltage and beam current. We describe an optimized workflow for FEBID tip fabrication (eight tips can be fabricated within 1-2 h) and demonstrate high-resolution and long-term stable HS-AFM imaging of annexin V and plasmid DNA using the FEBID tips fabricated in this study. We anticipate that this protocol may be useful for a wide range of AFM practitioners and facilitate the reproducible acquisition of high-resolution AFM data.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13334414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quality assessment and control of unprocessed anatomical, functional and diffusion MRI of the human brain using MRIQC 利用磁共振成像质量控制技术对未经处理的人脑解剖、功能和弥散MRI进行质量评估和控制。

IF 18.4 1区生物学

Nature Protocols Pub Date : 2026-05-11 DOI: 10.1038/s41596-026-01352-y

McKenzie P. Hagen, Céline Provins, Eilidh MacNicol, Jamie K. Li, Teresa Gomez, Mélanie Garcia, Saren H. Seeley, Jon Haitz Legarreta, Martin Norgaard, Patrick G. Bissett, Russell A. Poldrack, Ariel Rokem, Oscar Esteban

{"title":"Quality assessment and control of unprocessed anatomical, functional and diffusion MRI of the human brain using MRIQC","authors":"McKenzie P. Hagen, Céline Provins, Eilidh MacNicol, Jamie K. Li, Teresa Gomez, Mélanie Garcia, Saren H. Seeley, Jon Haitz Legarreta, Martin Norgaard, Patrick G. Bissett, Russell A. Poldrack, Ariel Rokem, Oscar Esteban","doi":"10.1038/s41596-026-01352-y","DOIUrl":"10.1038/s41596-026-01352-y","url":null,"abstract":"Quality control (QC) of magnetic resonance imaging (MRI) data before preprocessing is fundamental, because substandard data are known to introduce additional variability in the form of noise to subsequent analyses. This can result in spurious results of a false effect or the obstruction of a true effect. Consequently, there is a need for a reliable and robust method to identify subpar images, given pre-specified exclusion criteria. Here, we describe how to carry out the visual assessment of T1-weighted, T2-weighted, functional and diffusion MRI scans of the human brain with visual reports generated by MRIQC ( https://mriqc.readthedocs.io/en/stable/ ). We provide guidance and instructions for using the MRIQC software on all the images of the input dataset using typical research settings (i.e., a high-performance computing cluster). This includes installing MRIQC, configuring datasets (30–45 min active, plus 10–15 min of compute time per scan) and executing MRIQC (10–15 min compute time per scan). We then describe how to screen the visual reports generated with MRIQC to identify artifacts and potential quality issues and annotate the latter with the ‘rating widget’, a utility that enables rapid annotation and minimizes bookkeeping errors (1–5 min per participant). Integrating proper QC checks on the unprocessed data is fundamental to producing reliable statistical results and crucial to identifying faults in the scanning settings, preempting the acquisition of large datasets with persistent artifacts that should have been addressed as they emerged. MRIQC is software designed to help researchers assess the quality of reconstructed MRI scans before they undergo further data analysis. This protocol provides advice on how to use MRIQC for visual assessment of example artifacts.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":"21 10","pages":"4606-4634"},"PeriodicalIF":18.4,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147874976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0