Publications made with imaging support from NMI.


Silao FGS, Jiang T, Bereczky-Veress B, Kühbacher A, Ryman K, Uwamohoro N, Jenull S, Nogueira F, Ward M, Lion T, Urban CF, Rupp S, Kuchler K, Chen C, Peuckert C, Ljungdahl PO, “Proline catabolism is a key factor facilitating Candida albicans pathogenicity”, PLoS Pathog., 2023, 2;19(11):e1011677, doi: 10.1371/journal.ppat.1011677

Windhager J, Zanotelli VRT, Schulz D, Meyer L, Daniel M, Bodenmiller B, Eling N, “An end-to-end workflow for multiplexed image processing and analysis.”, Nat Protoc, 2023,

Unnersjö-Jess D, Ramdedovic A, Butt L, Plagmann I, Höhne M, Hackl A, Brismar H, Blom H, Schermer B, Benzing T, “Advanced optical imaging reveals preferred spatial orientation of podocyte processes along the axis of glomerular capillaries.”, Kidney Int., 2023,

Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Vuylsteke M, Stadler C, Eyckerman S, Spirohn K, Hao T, Calderwood MA, Gevaert K, “N-terminal proteoforms may engage in different protein complexes.”, Life Sci. Alliance, 2023, 6 (8),

Ramachandran M, Vaccaro A, van de Walle T, Georganaki M, Lugano R, Vemuri K, Kourougkiaouri D, Vazaios K, Hedlund M, Tsaridou G, Uhrbom L, Pietilä I, Martikainen M, van Hooren L, Olsson Bontell T, Jakola AS, Yu D, Westermark B, Essand M, Dimberg A, “Tailoring vascular phenotype through AAV therapy promotes anti-tumor immunity in glioma.”, Cancer Cell, 2023, 41 (6), 1134-1151.e10,

Sych T, Schlegel J, Barriga HMG, Ojansivu M, Hanke L, Weber F, Beklem Bostancioglu R, Ezzat K, Stangl H, Plochberger B, Laurencikiene J, El Andaloussi S, Fürth D, Stevens MM, Sezgin E, “High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler.”, Nat. Biotechnol., 2023,

Øvrebø Ø, Ojansivu M, Kartasalo K, Barriga HMG, Ranefall P, Holme MN, Stevens MM, “RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.”, BMC Bioinformatics, 2023, 24 (1), 237,

Sunadome K, Erickson AG, Kah D, Fabry B, Adori C, Kameneva P, Faure L, Kanatani S, Kaucka M, Dehnisch Ellström I, Tesarova M, Zikmund T, Kaiser J, Edwards S, Maki K, Adachi T, Yamamoto T, Fried K, Adameyko I, “Directionality of developing skeletal muscles is set by mechanical forces.”, Nat Commun, 2023, 14 (1), 3060,

Franzén Boger M, Benhach N, Hasselrot T, Brand RM, Rohan LC, Wang L, McGowan I, Edick S, Ho K, Meyn L, Matoba N, Palmer KE, Broliden K, Tjernlund A, “A topical rectal douche product containing Q-Griffithsin does not disrupt the epithelial border or alter CD4+ cell distribution in the human rectal mucosa.”, Sci Rep, 2023, 13 (1), 7547,

Pielawski N, Andersson A, Avenel C, Behanova A, Chelebian E, Klemm A, Nysjö F, Solorzano L, Wählby C, “TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data.”, Heliyon, 2023, 9 (5), e15306,

Li X, Andrusivova Z, Czarnewski P, Langseth CM, Andersson A, Liu Y, Gyllborg D, Braun E, Larsson L, Hu L, Alekseenko Z, Lee H, Avenel C, Kallner HK, Åkesson E, Adameyko I, Nilsson M, Linnarsson S, Lundeberg J, Sundström E, “Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.”, Nat. Neurosci., 2023, 26 (5), 891-901,

Schmied L, Luu TT, Søndergaard JN, Hald SH, Meinke S, Mohammad DK, Singh SB, Mayer C, Perinetti Casoni G, Chrobok M, Schlums H, Rota G, Truong HM, Westerberg LS, Guarda G, Alici E, Wagner AK, Kadri N, Bryceson YT, Saeed MB, Höglund P, “SHP-1 localization to the activating immune synapse promotes NK cell tolerance in MHC class I deficiency.”, Sci Signal, 2023, 16 (780), eabq0752,

Chotiwan N, Rosendal E, Willekens SMA, Schexnaydre E, Nilsson E, Lindqvist R, Hahn M, Mihai IS, Morini F, Zhang J, Ebel GD, Carlson L, Henriksson J, Ahlgren U, Marcellino D, Överby AK, “Type I interferon shapes brain distribution and tropism of tick-borne flavivirus.”, Nat Commun, 2023, 14 (1), 2007,

Larsson E, Morén B, McMahon KA, Parton RG, Lundmark R, “Dynamin2 functions as an accessory protein to reduce the rate of caveola internalization.”, J. Cell Biol., 2023, 222 (4),

Unnersjö-Jess D, Butt L, Höhne M, Sergei G, Fatehi A, Witasp A, Wernerson A, Patrakka J, Hoyer PF, Blom H, Schermer B, Bozek K, Benzing T, “Deep learning-based segmentation and quantification of podocyte foot process morphology suggests differential patterns of foot process effacement across kidney pathologies.”, Kidney Int., 2023,

Erickson A, Motta A, Kastriti ME, Edwards S, Lallemend F, Hadjab S, Ruhrberg C, Schwarz Q, Fried K, Bonanomi D, Adameyko I, “Motor nerves direct the development of the sympathetic nervous system”,, 2023,

Pierozan P, Kosnik M, Karlsson O, “High-content analysis shows synergistic effects of low perfluorooctanoic acid (PFOS) and perfluorooctane sulfonic acid (PFOA) mixture concentrations on human breast epithelial cell carcinogenesis.”, Environ Int, 2023, 172, 107746,

Sountoulidis A, Marco Salas S, Braun E, Avenel C, Bergenstråhle J, Theelke J, Vicari M, Czarnewski P, Liontos A, Abalo X, Andrusivová Ž, Mirzazadeh R, Asp M, Li X, Hu L, Sariyar S, Martinez Casals A, Ayoglu B, Firsova A, Michaëlsson J, Lundberg E, Wählby C, Sundström E, Linnarsson S, Lundeberg J, Nilsson M, Samakovlis C, “A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.”, Nat Cell Biol, 2023, 25 (2), 351-365,

Forsberg KM, Graffmo KS, Stenvall E, Tabikh N, Marklund SL, Brännström T, Andersen PM, “Widespread CNS pathology in amyotrophic lateral sclerosis homozygous for the D90A SOD1 mutation”, Acta Neuropathol, 2023, 145 (1), 13-28,

Behanova A, Avenel C, Andersson A, Chelebian E, Klemm A, Wik L, Östman A, Wählby C, “Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3”, Biol. Imaging, 2023, 3,


Nordenström M, Benselfelt T, Hollertz R, Wennmalm S, Larsson PA, Mehandzhiyski A, Rolland N, Zozoulenko I, Söderberg D, Wågberg L, “The structure of cellulose nanofibril networks at low concentrations and their stabilizing action on colloidal particles.”, Carbohydr Polym, 2022, 297, 120046,

Crescitelli R, Filges S, Karimi N, Urzì O, Alonso-Agudo T, Ståhlberg A, Lötvall J, Lässer C, Olofsson Bagge R, “Extracellular vesicle DNA from human melanoma tissues contains cancer-specific mutations.”, Front Cell Dev Biol, 2022, 10, 1028854,

Moffitt JR, Lundberg E, Heyn H, “The emerging landscape of spatial profiling technologies.”, Nat. Rev. Genet., 2022, 23 (12), 741-759,

Bonilla JC, Sørensen JL, Warming AS, Clausen MP, “Quantitative image analysis of protein foam microstructure and its correlation with rheological properties: Egg white foam”, Food Hydrocolloids, 2022, 133, 108010,

Nicoś M, Harbers L, Patrucco E, Kramer-Drauberg M, Zhang X, Voena C, Kowalczyk A, Bożyk A, Pęksa R, Jarosz B, Szumiło J, Simonetti M, Żuk M, Wasąg B, Reszka K, Duchnowska R, Milanowski J, Chiarle R, Bienko M, Krawczyk P, Jassem J, Ambrogio C, Crosetto N, “Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases.”, JTO Clin Res Rep, 2022, 3 (12), 100435,

Tonge JJ, Notley SV, Dunning MJ, López-Guajardo A, Medcalf JD, Heldin P, Panoutsos G, Gad AKB, “Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo.”, Sci Rep, 2022, 12 (1), 19835,

Leyhr J, Waldmann L, Filipek-Górniok B, Zhang H, Allalou A, Haitina T, “A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint.”, Elife, 2022, 11,

Maurya DK, Berghard A, Bohm S, “A multivesicular body-like organelle mediates stimulus-regulated trafficking of olfactory ciliary transduction proteins.”, Nat Commun, 2022, 13 (1), 6889,

Mota A, Berezicki S, Wernersson E, Harbers L, Li-Wang X, Gradin K, Peuckert C, Crosetto N, Bienko M, “FRET-FISH probes chromatin compaction at individual genomic loci in single cells.”, Nat Commun, 2022, 13 (1), 6680,

Schneider KL, Ahmadpour D, Keuenhof KS, Eisele-Bürger AM, Berglund LL, Eisele F, Babazadeh R, Höög JL, Nyström T, Widlund PO, “Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates.”, J. Biol. Chem., 2022, 298 (11), 102476,

Gineste C, Youhanna S, Vorrink SU, Henriksson S, Hernández A, Cheng AJ, Chaillou T, Buttgereit A, Schneidereit D, Friedrich O, Hultenby K, Bruton JD, Ivarsson N, Sandblad L, Lauschke VM, Westerblad H, “Enzymatically dissociated muscle fibers display rapid dedifferentiation and impaired mitochondrial calcium control”, iScience, 2022, 105654,

Michno W, Koutarapu S, Camacho R, Toomey C, Stringer K, Minta K, Ge J, Jha D, Fernandez-Rodriguez J, Brinkmalm G, Zetterberg H, Blennow K, Ryan NS, Lashley T, Hanrieder J, “Chemical traits of cerebral amyloid angiopathy in familial British-, Danish-, and non-Alzheimer’s dementias.”, J. Neurochem., 2022, 163 (3), 233-246,

Schlegel J, Porebski B, Andronico L, Hanke L, Edwards S, Brismar H, Murrell B, McInerney G, Fernandez-Capetillo O, Sezgin E, “A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens”,, 2022,

Koutarapu S, Ge J, Jha D, Blennow K, Zetterberg H, Lashley T, Michno W, Hanrieder J, “Correlative Chemical Imaging Identifies Amyloid Peptide Signatures of Neuritic Plaques and Dystrophy in Human Sporadic Alzheimer’s Disease.”, Brain Connect, 2022,

Iribarren C, Nordlander S, Sundin J, Isaksson S, Savolainen O, Törnblom H, Magnusson MK, Simrén M, Öhman L, “Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids.”, Neurogastroenterol. Motil., 2022, 34 (10), e14390,

Dolan B, Ermund A, Martinez-Abad B, Johansson MEV, Hansson GC, “Clearance of small intestinal crypts involves goblet cell mucus secretion by intracellular granule rupture and enterocyte ion transport.”, Sci Signal, 2022, 15 (752), eabl5848,

Ruiz M, Svensk E, Einarsson E, Grahn EP, Pilon M, “A small molecule screen for paqr-2 suppressors identifies Tyloxapol as a membrane fluidizer for C. elegans and mammalian cells.”, Biochimica et Biophysica Acta (BBA) – Biomembranes, 2022, 1864 (9), 183959,

Waldmann L, Leyhr J, Zhang H, Allalou A, Öhman-Mägi C, Haitina T, “The role of Gdf5 in the development of the zebrafish fin endoskeleton.”, Dev. Dyn., 2022, 251 (9), 1535-1549,

Song J, Nilsson G, Xu Y, Zelco A, Rocha-Ferreira E, Wang Y, Zhang X, Zhang S, Ek J, Hagberg H, Zhu C, Wang X, “Temporal brain transcriptome analysis reveals key pathological events after germinal matrix hemorrhage in neonatal rats.”, J. Cereb. Blood Flow Metab., 2022, 42 (9), 1632-1649,

Ragaller F, Andronico L, Sykora J, Kulig W, Rog T, Urem YB, Danylchuk DI, Hof M, Klymchenko A, Amaro M, Vattulainen I, Sezgin E, “Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties.”, Open Biol, 2022, 12 (9), 220175,

Bekkhus T, Avenel C, Hanna S, Franzén Boger M, Klemm A, Bacovia DV, Wärnberg F, Wählby C, Ulvmar MH, “Automated detection of vascular remodeling in tumor-draining lymph nodes by the deep-learning tool HEV-finder.”, J. Pathol., 2022, 258 (1), 4-11,

Raykova D, Kermpatsou D, Malmqvist T, Harrison PJ, Sander MR, Stiller C, Heldin J, Leino M, Ricardo S, Klemm A, David L, Spjuth O, Vemuri K, Dimberg A, Sundqvist A, Norlin M, Klaesson A, Kampf C, Söderberg O, “A method for Boolean analysis of protein interactions at a molecular level.”, Nat Commun, 2022, 13 (1), 4755,

Gupta A, Sabirsh A, Wahlby C, Sintorn IM, “SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images.”, IEEE J Biomed Health Inform, 2022, 26 (8), 4079-4089,

Mund A, Coscia F, Kriston A, Hollandi R, Kovács F, Brunner AD, Migh E, Schweizer L, Santos A, Bzorek M, Naimy S, Rahbek-Gjerdrum LM, Dyring-Andersen B, Bulkescher J, Lukas C, Eckert MA, Lengyel E, Gnann C, Lundberg E, Horvath P, Mann M, “Deep Visual Proteomics defines single-cell identity and heterogeneity.”, Nat. Biotechnol., 2022, 40 (8), 1231-1240,

Marco Salas S, Yuan X, Sylven C, Nilsson M, Wählby C, Partel G, “De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.”, PLoS Comput. Biol., 2022, 18 (8), e1010366,

Haase R, Fazeli E, Legland D, Doube M, Culley S, Belevich I, Jokitalo E, Schorb M, Klemm A, Tischer C, “A Hitchhiker’s guide through the bio-image analysis software universe.”, FEBS Lett., 2022,

Stenberg S, Li J, Gjuvsland AB, Persson K, Demitz-Helin E, González Peña C, Yue JX, Gilchrist C, Ärengård T, Ghiaci P, Larsson-Berglund L, Zackrisson M, Smits S, Hallin J, Höög JL, Molin M, Liti G, Omholt SW, Warringer J, “Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation.”, Elife, 2022, 11,

Banerjee D, Nayakawde NB, Antony D, Deshmukh M, Ghosh S, Sihlbom C, Berger E, Ul Haq U, Olausson M, “Characterization of Decellularized Implants for Extracellular Matrix Integrity and Immune Response Elicitation.”, Tissue Eng Part A, 2022, 28 (13-14), 621-639,

Kouznetsova A, Liu JG, Valentiniene S, Brismar H, Höög C, “Age-dependent aneuploidy in mammalian oocytes instigated at the second meiotic division.”, Aging Cell, 2022, 21 (7), e13649,

Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hällberg BM, Falkenberg M, “Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization.”, Cell, 2022, 185 (13), 2309-2323.e24,

Arnold H, Panara V, Hußmann M, Filipek-Gorniok B, Skoczylas R, Ranefall P, Gloger M, Allalou A, Hogan BM, Schulte-Merker S, Koltowska K, “mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners.”, Cell Rep, 2022, 39 (12), 110982,

Verhoeven BM, Mei S, Olsen TK, Gustafsson K, Valind A, Lindström A, Gisselsson D, Fard SS, Hagerling C, Kharchenko PV, Kogner P, Johnsen JI, Baryawno N, “The immune cell atlas of human neuroblastoma.”, Cell Reports Medicine, 2022, 3 (6), 100657,

Hübner B, von Otter E, Ahsan B, Wee ML, Henriksson S, Ludwig A, Sandin S, “Ultrastructure and nuclear architecture of telomeric chromatin revealed by correlative light and electron microscopy.”, Nucleic Acids Res., 2022, 50 (9), 5047-5063,

Larsson S, Kettunen P, Carén H, “Orthotopic Transplantation of Human Paediatric High-Grade Glioma in Zebrafish Larvae.”, Brain Sci, 2022, 12 (5),

Elebring E, Wallenius V, Casselbrant A, Docherty NG, Roux CWL, Marschall HU, Fändriks L, “A Fatty Diet Induces a Jejunal Ketogenesis Which Inhibits Local SGLT1-Based Glucose Transport via an Acetylation Mechanism-Results from a Randomized Cross-Over Study between Iso-Caloric High-Fat versus High-Carbohydrate Diets in Healthy Volunteers.”, Nutrients, 2022, 14 (9),

Julner A, Abbasi M, Menéndez-Benito V, “The microtubule plus-end tracking protein Bik1 is required for chromosome congression.”, Mol. Biol. Cell, 2022, 33 (5), br7,

Bradley F, Franzén Boger M, Kaldhusdal V, Åhlberg A, Edfeldt G, Lajoie J, Bergström S, Omollo K, Damdimopoulos A, Czarnewski P, Månberg A, Oyugi J, Kimani J, Nilsson P, Fowke K, Tjernlund A, Broliden K, “Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate.”, PLoS Pathog., 2022, 18 (5), e1010494,

Ichioka Y, Derks J, Dahlén G, Berglundh T, Larsson L, “Mechanical removal of biofilm on titanium discs: An in vitro study.”, J. Biomed. Mater. Res. Part B Appl. Biomater., 2022, 110 (5), 1044-1055,

Nair S, Leverin AL, Rocha-Ferreira E, Sobotka KS, Thornton C, Mallard C, Hagberg H, “Induction of Mitochondrial Fragmentation and Mitophagy after Neonatal Hypoxia-Ischemia.”, Cells, 2022, 11 (7),

Hallberg I, Persson S, Olovsson M, Moberg M, Ranefall P, Laskowski D, Damdimopoulou P, Sirard M, Rüegg J, Sjunnesson YCB, “Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro.”, Reprod Toxicol, 2022, 109, 19-30,

Kaimal JM, Tampere M, Le TH, Axelsson U, Xu H, Axelsson H, Bäckström A, Marabita F, Moussaud-Lamodière E, Njenda D, Sepulveda CO, Oyuang W, Seashore-Ludlow B, Vernersson C, Mirazimi A, Lundberg E, Östling P, Stadler C, “Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing”,, 2022,

Cuéllar J, Vallin J, Svanström A, Maestro-López M, Bueno-Carrasco MT, Ludlam WG, Willardson BM, Valpuesta JM, Grantham J, “The Molecular Chaperone CCT Sequesters Gelsolin and Protects it from Cleavage by Caspase-3.”, J. Mol. Biol., 2022, 434 (5), 167399,

Brodin ATS, Gabulya S, Wellfelt K, Karlsson TE, “Five Hours Total Sleep Deprivation Does Not Affect CA1 Dendritic Length or Spine Density.”, Front. Synaptic Neurosci., 2022, 14, 854160,

Schmied L, Luu TT, Søndergaard JN, Meinke S, Mohammad DK, Singh SB, Mayer C, Casoni GP, Chrobok M, Schlums H, Rota G, Truong HM, Westerberg LS, Guarda G, Alici E, Wagner AK, Kadri N, Bryceson YT, Saeed MB, Höglund P, “Control of NK cell tolerance in MHC class I-deficiency by regulated SHP-1 localization to the activating immune synapse”,, 2022,

Stenudd M, Sabelström H, Llorens-Bobadilla E, Zamboni M, Blom H, Brismar H, Zhang S, Basak O, Clevers H, Göritz C, Barnabé-Heider F, Frisén J, “Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.”, Cell Rep, 2022, 38 (9), 110440,

Kay E, Stulz R, Becquart C, Lovric J, Tängemo C, Thomen A, Baždarević D, Najafinobar N, Dahlén A, Pielach A, Fernandez-Rodriguez J, Strömberg R, Ämmälä C, Andersson S, Kurczy M, “NanoSIMS Imaging Reveals the Impact of Ligand-ASO Conjugate Stability on ASO Subcellular Distribution.”, Pharmaceutics, 2022, 14 (2), 463,

Mota A, Schweitzer M, Wernersson E, Crosetto N, Bienko M, “Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.”, Sci Data, 2022, 9 (1), 47,

Nadeem A, Berg A, Pace H, Alam A, Toh E, Ådén J, Zlatkov N, Myint SL, Persson K, Gröbner G, Sjöstedt A, Bally M, Barandun J, Uhlin BE, Wai SN, “Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae.”, Elife, 2022, 11,

Wernersson E, Gelali E, Girelli G, Wang S, Castillo D, Langseth CM, Nguyen H, Chattoraj S, Casals AM, Lundberg E, Nilsson M, Marti-Renom M, Wu Ct, Crosetto N, Bienko M, “Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images”,, 2022,

Jalalvand E, Alvelid J, Coceano G, Edwards S, Robertson B, Grillner S, Testa I, “ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal.”, Elife, 2022, 11,

Michno W, Wehrli PM, Koutarapu S, Marsching C, Minta K, Ge J, Meyer SW, Zetterberg H, Blennow K, Henkel C, Oetjen J, Hopf C, Hanrieder J, “Structural amyloid plaque polymorphism is associated with distinct lipid accumulations revealed by trapped ion mobility mass spectrometry imaging.”, J. Neurochem., 2022, 160 (4), 482-498,

Aswendt M, Wilhelmsson U, Wieters F, Stokowska A, Schmitt FJ, Pallast N, de Pablo Y, Mohammed L, Hoehn M, Pekna M, Pekny M, “Reactive astrocytes prevent maladaptive plasticity after ischemic stroke.”, Prog Neurobiol, 2022, 209, 102199,

Thomsen C, Malfatti E, Jovanovic A, Roberts M, Kalev O, Lindberg C, Oldfors A, “Proteomic characterisation of polyglucosan bodies in skeletal muscle in RBCK1 deficiency.”, Neuropathol Appl Neurobiol, 2022, 48 (1), e12761,

Habicher J, Varshney GK, Waldmann L, Snitting D, Allalou A, Zhang H, Ghanem A, Öhman Mägi C, Dierker T, Kjellén L, Burgess SM, Ledin J, “Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development.”, PLoS Genet., 2022, 18 (2), e1010067,

Behanova A, Klemm A, Wählby C, “Spatial Statistics for Understanding Tissue Organization.”, Front Physiol, 2022, 13, 832417,

Bäcklund FG, Schmuck B, Miranda GHB, Greco G, Pugno NM, Rydén J, Rising A, “An Image-Analysis-Based Method for the Prediction of Recombinant Protein Fiber Tensile Strength.”, Materials (Basel), 2022, 15 (3),

Enrico A, Voulgaris D, Östmans R, Sundaravadivel N, Moutaux L, Cordier A, Niklaus F, Herland A, Stemme G, “3D Microvascularized Tissue Models by Laser-Based Cavitation Molding of Collagen.”, Adv Mater, 2022, e2109823,

Ekström K, Crescitelli R, Pétursson HI, Johansson J, Lässer C, Olofsson Bagge R, “Characterization of surface markers on extracellular vesicles isolated from lymphatic exudate from patients with breast cancer.”, BMC Cancer, 2022, 22 (1), 50,

Stoltenborg I, Peris-Sampedro F, Schéle E, Le May MV, Adan RAH, Dickson SL, “TRAPing Ghrelin-Activated Circuits: A Novel Tool to Identify, Target and Control Hormone-Responsive Populations in TRAP2 Mice.”, Int J Mol Sci, 2022, 23 (1),

Butt L, Unnersjö-Jess D, Höhne M, Hahnfeldt R, Reilly D, Rinschen MM, Plagmann I, Diefenhardt P, Brähler S, Brinkkötter PT, Brismar H, Blom H, Schermer B, Benzing T, “Super-Resolution Imaging of the Filtration Barrier Suggests a Role for Podocin R229Q in Genetic Predisposition to Glomerular Disease.”, J. Am. Soc. Nephrol., 2022, 33 (1), 138-154,

Wang Y, Acs B, Robertson S, Liu B, Solorzano L, Wählby C, Hartman J, Rantalainen M, “Improved breast cancer histological grading using deep learning.”, Ann. Oncol., 2022, 33 (1), 89-98,

Klemm A, Miura K, “Batch Processing Methods in ImageJ”, Springer, 2022, 7-27,

Makasewicz K, Wennmalm S, Linse S, Sparr E, “Alfa-Synuclein-induced deformation of small unilamellar vesicles”, QRB Discovery, 2022, 3,


Rabasco S, Nguyen TDK, Gu C, Kurczy ME, Phan NTN, Ewing AG, “Localization and Absolute Quantification of Dopamine in Discrete Intravesicular Compartments Using NanoSIMS Imaging.”, Int J Mol Sci, 2021, 23 (1),

Pozo-Rodrigálvarez A, Li Y, Stokowska A, Wu J, Dehm V, Sourkova H, Steinbusch H, Mallard C, Hagberg H, Pekny M, Pekna M, “C3a Receptor Signaling Inhibits Neurodegeneration Induced by Neonatal Hypoxic-Ischemic Brain Injury.”, Front Immunol, 2021, 12, 768198,

Omrani A, de Vrind VAJ, Lodder B, Stoltenborg I, Kooij K, Wolterink-Donselaar IG, Luijendijk-Berg MCM, Garner KM, Van’t Sant LJ, Rozeboom A, Dickson SL, Meye FJ, Adan RAH, “Identification of Novel Neurocircuitry Through Which Leptin Targets Multiple Inputs to the Dopamine System to Reduce Food Reward Seeking.”, Biol. Psychiatry, 2021, 90 (12), 843-852,

Carravilla P, Dasgupta A, Zhurgenbayeva G, Danylchuk DI, Klymchenko AS, Sezgin E, Eggeling C, “Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes.”, Biophysical Reports, 2021, 1 (2), None,

Unnersjö-Jess D, Ramdedovic A, Höhne M, Butt L, Koehler FC, Müller RU, Hoyer PF, Blom H, Schermer B, Benzing T, “Three-Dimensional Super-Resolved Imaging of Paraffin-Embedded Kidney Samples”, Kidney360, 2021, 10.34067/KID.0005882021,

Barmpatsalou V, Dubbelboer IR, Rodler A, Jacobson M, Karlsson E, Pedersen BL, Bergström CAS, “Physiological properties, composition and structural profiling of porcine gastrointestinal mucus.”, Eur J Pharm Biopharm, 2021, 169, 156-167,

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Zhang H, Ericsson M, Virtanen M, Weström S, Wählby C, Vahlquist A, Törmä H, “Quantitative image analysis of protein expression and colocalisation in skin sections”, Exp Dermatol, 2018, 27 (2), 196-199,

Schroeder BO, Birchenough GMH, Ståhlman M, Arike L, Johansson MEV, Hansson GC, Bäckhed F, “Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration.”, Cell Host Microbe, 2018, 23 (1), 27-40.e7,

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Matuszewski DJ, Hast A, Wählby C, Sintorn IM, “A short feature vector for image matching: The Log-Polar Magnitude feature descriptor.”, PLoS ONE, 2017, 12 (11), e0188496,

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Sadanandan SK, Karlsson J, Wahlby C, “Spheroid Segmentation Using Multiscale Deep Adversarial Networks”, The IEEE International Conference on Computer Vision (ICCV), 2017, 2017, 36-41,

Edfeldt G, Lajoie J, Röhl M, Tjernlund A, “Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis”, Scand J Immunol, 2017, 86 (4), 249-350

Forslid G, Wieslander H, Bengtsson E, Wahlby C, Hirsch JM, Stark CR, Sadanandan SK, “Deep Convolutional Neural Networks for Detecting Cellular Changes Due to Malignancy”, The IEEE International Conference on Computer Vision (ICCV), 2017, 2017,

Sun JB, Holmgren J, Larena M, Terrinoni M, Fang Y, Bresnick AR, Xiang Z, “Deficiency in Calcium-Binding Protein S100A4 Impairs the Adjuvant Action of Cholera Toxin.”, Front Immunol, 2017, 8, 1119,

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Gliga AR, Edoff K, Caputo F, Källman T, Blom H, Karlsson HL, Ghibelli L, Traversa E, Ceccatelli S, Fadeel B, “Cerium oxide nanoparticles inhibit differentiation of neural stem cells.”, Sci Rep, 2017, 7 (1), 9284,

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Liu W, Li H, Edin F, Brännström J, Glueckert R, Schrott-Fischer A, Molnar M, Pacholsky D, Pfaller K, Rask-Andersen H, “Molecular composition and distribution of gap junctions in the sensory epithelium of the human cochlea-a super-resolution structured illumination microscopy (SR-SIM) study.”, Ups. J. Med. Sci., 2017, 122 (3), 160-170,

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Borglin J, Selegård R, Aili D, Ericson MB, “Peptide Functionalized Gold Nanoparticles as a Stimuli Responsive Contrast Medium in Multiphoton Microscopy.”, Nano Lett., 2017, 17 (3), 2102-2108,

Birchenough GM, Dalgakiran F, Witcomb LA, Johansson ME, McCarthy AJ, Hansson GC, Taylor PW, “Postnatal development of the small intestinal mucosa drives age-dependent, regio-selective susceptibility to Escherichia coli K1 infection.”, Sci Rep, 2017, 7 (1), 83,

Reuss M, Fördős F, Blom H, Öktem O, Högberg B, Brismar H, “Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures”, New J. Phys., 2017, 19 (2), 025013,

Alkasalias T, Alexeyenko A, Hennig K, Danielsson F, Lebbink RJ, Fielden M, Turunen SP, Lehti K, Kashuba V, Madapura HS, Bozoky B, Lundberg E, Balland M, Guvén H, Klein G, Gad AK, Pavlova T, “RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.”, Proc. Natl. Acad. Sci. U.S.A., 2017, 114 (8), E1413-E1421,

Kaya I, Brinet D, Michno W, Syvänen S, Sehlin D, Zetterberg H, Blennow K, Hanrieder J, “Delineating Amyloid Plaque Associated Neuronal Sphingolipids in Transgenic Alzheimer’s Disease Mice (tgArcSwe) Using MALDI Imaging Mass Spectrometry.”, ACS Chem Neurosci, 2017, 8 (2), 347-355,

Risal S, Zhang J, Adhikari D, Liu X, Shao J, Hu M, Busayavalasa K, Tu Z, Chen Z, Kaldis P, Liu K, “MASTL is essential for anaphase entry of proliferating primordial germ cells and establishment of female germ cells in mice.”, Cell Discov, 2017, 3 (1), 16052,

Stokowska A, Atkins AL, Morán J, Pekny T, Bulmer L, Pascoe MC, Barnum SR, Wetsel RA, Nilsson JA, Dragunow M, Pekna M, “Complement peptide C3a stimulates neural plasticity after experimental brain ischaemia.”, Brain, 2017, 140 (2), 353-369,

Blockhuys S, Wittung-Stafshede P, “Copper chaperone Atox1 plays role in breast cancer cell migration.”, Biochem. Biophys. Res. Commun., 2017, 483 (1), 301-304,

Dolatabadi S, Candia J, Akrap N, Vannas C, Tesan Tomic T, Losert W, Landberg G, Åman P, Ståhlberg A, “Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level.”, Front Genet, 2017, 8, 1,

Terriac E, Coceano G, Mavajian Z, Hageman T, Christ A, Testa I, Lautenschläger F, Gad A, “Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts”, Cells, 2017, 6 (1), 2,

Skogs M, Stadler C, Schutten R, Hjelmare M, Gnann C, Björk L, Poser I, Hyman A, Uhlén M, Lundberg E, “Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.”, J. Proteome Res., 2017, 16 (1), 147-155,

Ishaq O, Sadanandan SK, Wählby C, “Deep Fish: Deep Learning–Based Classification of Zebrafish Deformation for High-Throughput Screening”, SLAS DISCOVERY: Advancing Life Sciences R&D, 2017, 22 (1), 102-107,

Schizas N, Perry S, Andersson B, Wählby C, Kullander K, Hailer NP, “Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury”, Neuroimmunomodulation, 2017, 24 (4-5), 220-230,

Bombrun M, Ranefall P, Lindblad J, Allalou A, Partel G, Solorzano L, Qian X, Nilsson M, Wählby C, “Decoding Gene Expression in 2D and 3D”, Scandinavian Conference on Image Analysis 2017, 2017, 257-268,


Villamil Giraldo AM, Fyrner T, Wennmalm S, Parikh AN, Öllinger K, Ederth T, “Spontaneous Vesiculation and pH-Induced Disassembly of a Lysosomotropic Detergent: Impacts on Lysosomotropism and Lysosomal Delivery.”, Langmuir, 2016, 32 (50), 13566-13575,

Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R, “The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.”, J. Cell Biol., 2016, 215 (4), 543-558,

Gibbs A, Buggert M, Ranefall P, Introini A, Cheuk S, Eidsmo L, Hirbod T, Ball T, Kimani J, Kaul R, Karlsson AC, Wählby C, Broliden K, Tjernlund A, “Analysis of the Distribution of CD103 on CD8 T Cells in Blood and Genital Mucosa of HIVinfected Female Sex Workers”, Conference on HIV Research for Prevention (HIV R4P), 2016, October 17–20, Chicago, 2016

Blom H, Bernhem K, Brismar H, “Sodium pump organization in dendritic spines.”, Neurophotonics, 2016, 3 (4), 041803,

Nagaraj V, Kazim AS, Helgeson J, Lewold C, Barik S, Buda P, Reinbothe TM, Wennmalm S, Zhang E, Renström E, “Elevated Basal Insulin Secretion in Type 2 Diabetes Caused by Reduced Plasma Membrane Cholesterol.”, Mol. Endocrinol., 2016, 30 (10), 1059-1069,

, “Abstracts of the HIV Research for Prevention Meeting, HIVR4P, 17-20 October, 2016, Chicago, USA”, AIDS Research and Human Retroviruses, 2016, 32 (S1), 1-409,

Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, Yamamoto T, “A proposal for validation of antibodies.”, Nat. Methods, 2016, 13 (10), 823-827,

Nejedla M, Sadi S, Sulimenko V, de Almeida FN, Blom H, Draber P, Aspenström P, Karlsson R, “Profilin connects actin assembly with microtubule dynamics.”, Mol. Biol. Cell, 2016, 27 (15), 2381-2393,

Kaucka M, Ivashkin E, Gyllborg D, Zikmund T, Tesarova M, Kaiser J, Xie M, Petersen J, Pachnis V, Nicolis SK, Yu T, Sharpe P, Arenas E, Brismar H, Blom H, Clevers H, Suter U, Chagin AS, Fried K, Hellander A, Adameyko I, “Analysis of neural crest-derived clones reveals novel aspects of facial development.”, Sci Adv, 2016, 2 (8), e1600060,

Liu W, Edin F, Blom H, Magnusson P, Schrott-Fischer A, Glueckert R, Santi PA, Li H, Laurell G, Rask-Andersen H, “Super-resolution structured illumination fluorescence microscopy of the lateral wall of the cochlea: the Connexin26/30 proteins are separately expressed in man.”, Cell Tissue Res., 2016, 365 (1), 13-27,

Burlaka I, Nilsson LM, Scott L, Holtbäck U, Eklöf AC, Fogo AB, Brismar H, Aperia A, “Prevention of apoptosis averts glomerular tubular disconnection and podocyte loss in proteinuric kidney disease.”, Kidney Int., 2016, 90 (1), 135-148,

Agostinho A, Manneberg O, van Schendel R, Hernández-Hernández A, Kouznetsova A, Blom H, Brismar H, Höög C, “High density of REC8 constrains sister chromatid axes and prevents illegitimate synaptonemal complex formation.”, EMBO Rep., 2016, 17 (6), 901-913,

Vanherberghen B, Frisk T, Forslund E, Olofsson PE, Guldevall K, Önfelt B, “Microwell-Based Live Cell Imaging of NK Cell Dynamics to Assess Heterogeneity in Motility and Cytotoxic Response.”, Methods Mol. Biol., 2016, 1441, 87-106,

Guldevall K, Brandt L, Forslund E, Olofsson K, Frisk TW, Olofsson PE, Gustafsson K, Manneberg O, Vanherberghen B, Brismar H, Kärre K, Uhlin M, Önfelt B, “Microchip Screening Platform for Single Cell Assessment of NK Cell Cytotoxicity.”, Front Immunol, 2016, 7, 119,

Rabasovic MD, Sisamakis E, Wennmalm S, Widengren J, “Label-Free Fluctuation Spectroscopy Based on Coherent Anti-Stokes Raman Scattering from Bulk Water Molecules.”, Chemphyschem, 2016, 17 (7), 1025-1033,

Aperia A, Akkuratov EE, Fontana JM, Brismar H, “Na+-K+-ATPase, a new class of plasma membrane receptors.”, Am. J. Physiol., Cell Physiol., 2016, 310 (7), C491-C495,

Ranefall P, Wählby C, “Global gray-level thresholding based on object size.”, Cytometry A, 2016, 89 (4), 385-390,

Schedin-Weiss S, Caesar I, Winblad B, Blom H, Tjernberg LO, “Super-resolution microscopy reveals γ-secretase at both sides of the neuronal synapse.”, Acta Neuropathol Commun, 2016, 4, 29,

Holm A, Magnusson KE, Vikström E, “Pseudomonas aeruginosa N-3-oxo-dodecanoyl-homoserine Lactone Elicits Changes in Cell Volume, Morphology, and AQP9 Characteristics in Macrophages”, Front. Cell. Infect. Microbiol., 2016, 6,

Matuszewski DJ, Wählby C, Puigvert JC, Sintorn IM, “PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data.”, PLoS ONE, 2016, 11 (3), e0151554,

Navarro JR, Wennmalm S, Godfrey J, Breitholtz M, Edlund U, “Luminescent Nanocellulose Platform: From Controlled Graft Block Copolymerization to Biomarker Sensing.”, Biomacromolecules, 2016, 17 (3), 1101-1109,

Turdalieva A, Solandt J, Shambetova N, Xu H, Blom H, Brismar H, Zelenina M, Fu Y, “Bioelectric and Morphological Response of Liquid-Covered Human Airway Epithelial Calu-3 Cell Monolayer to Periodic Deposition of Colloidal 3-Mercaptopropionic-Acid Coated CdSe-CdS/ZnS Core-Multishell Quantum Dots.”, PLoS ONE, 2016, 11 (2), e0149915,

Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS, “Systems Proteomics View of the Endogenous Human Claudin Protein Family.”, J. Proteome Res., 2016, 15 (2), 339-359,

Sadanandan SK, Baltekin O, Magnusson KEG, Boucharin A, Ranefall P, Jalden J, Elf J, Wahlby C, “Segmentation and Track-Analysis in Time-Lapse Imaging of Bacteria”, IEEE J. Sel. Top. Signal Process., 2016, 10 (1), 174-184,

Unnersjö-Jess D, Scott L, Blom H, Brismar H, “Super-resolution stimulated emission depletion imaging of slit diaphragm proteins in optically cleared kidney tissue.”, Kidney Int., 2016, 89 (1), 243-247,

Sadanandan SK, Ranefall P, Wählby C, “Feature Augmented Deep Neural Networks for Segmentation of Cells”,, 2016, 231-243,

Mignardi M, Ishaq O, Qian X, Wahlby C, “Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics”, Proc. IEEE, 2016, 1-12,

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