Image Analyst MKII provides complex image processing tasks in a biologist-friendly manner.

Fluorescence microscopy image analysis
automation - time series - physiology

Publications using Image Analyst MKII

Image Analyst MKII or algorithms implemented in Image Analyst MKII have been used in the following publications:

  1. Gerencser, A.A. and Adam-Vizi, V. (2001). Selective, High-Resolution Fluorescence Imaging of  Mitochondrial Ca2+ Concentration. Cell Calcium. 30.5:311-321.
  2. Chinopoulos C, Gerencser AA, Doczi J, Fiskum G, Adam-Vizi V. Inhibition of glutamate-induced delayed calcium deregulation by 2-APB and La3+ in cultured cortical neurones. J. Neurochem. 2004 Oct;91(2):471–83.
  3. Gerencser A.A., Adam-Vizi V. Mitochondrial Ca2+ dynamics reveals limited intramitochondrial Ca2+ diffusion. Biophys. J. 2005 Jan;88(1):698–714.
  4. Barsoum MJ, Yuan H, Gerencser AA, Liot G, Kushnareva Y, Graber S, Kovacs I, Lee WD, Waggoner J, Cui J, White AD, Bossy B, Martinou J-CC, Youle RJ, Lipton SA, Ellisman MH, Perkins GA, Bossy-Wetzel E, Gräber S. Nitric oxide-induced mitochondrial fission is regulated by dynamin-related GTPases in neurons. EMBO J. 2006 Aug 23;25(16):3900–11.
  5. Yuan H, Gerencser AA, Liot G, Lipton SA, Ellisman M, Perkins GA, Bossy-Wetzel E. Mitochondrial fission is an upstream and required event for bax foci formation in response to nitric oxide in cortical neurons. Cell Death Differ. 2007 Mar;14(3):462–71.
  6. Gerencser, A.A., Doczi, J., Töröcsik, B., Bossy-Wetzel, E., and Adam-Vizi, V. (2008). Mitochondrial Swelling Measurement in Situ by Optimized Spatial Filtering: Astrocyte-Neuron Differences. Biophys J. 2008 Sep;95(5):2583-98.
  7. Gerencser A. A. and Nicholls D. G. (2008) Measurement of Instantaneous Velocity Vectors of Organelle Transport: Mitochondrial Transport and Bioenergetics in Hippocampal Neurons. Biophys J. 2008 Sep 15;95(6):3079-99.
  8. Choi S.W., Gerencser A.A., Nicholls D.G. (2009) Bioenergetic analysis of isolated cerebrocortical nerve terminals on a microgram scale: spare respiratory capacity and stochastic mitochondrial failure. J Neurochem. 2009 May;109(4):1179-91
  9. Gerencser A. A., Mark KA, Hubbard AE, Divakaruni AS, Mehrabian Z, Nicholls DG, Polster BM  (2009) Real-time Visualization of Cytoplasmic Calpain Activation and Calcium Deregulation in Acute Glutamate Excitotoxicity. J Neurochem. 2009 Aug;110(3):990-1004
  10. Konràd C, Kiss G, Töröcsik B, Lábár JL, Gerencser AA, Mándi M, Adam-Vizi V, Chinopoulos C. (2011) A distinct sequence in the adenine nucleotide translocase from Artemia franciscana embryos is associated with insensitivity to bongkrekate and atypical effects of adenine nucleotides on Ca(2+) uptake and sequestration. FEBS J.
  11. Doczi J, Turiak L, Vajda S, Mandi M, Torocsik B, Gerencser AA, Kiss G, Konrad C, Adam-Vizi V, Chinopoulos C. (2011) Complex contribution of cyclophilin D to Ca2+-induced permeability transition in brain mitochondria, with relation to the bioenergetic state. J. Biol. Chem.  2011 Feb 25;286(8):6345-53
  12. Affourtit C, Jastroch M, Brand MD. Uncoupling protein-2 attenuates glucose-stimulated insulin secretion in INS-1E insulinoma cells by lowering mitochondrial reactive oxygen species. Free Radic Biol Med. Elsevier Inc.; 2011 Mar 1;50(5):609–16.  
  13. Choi SW, Gerencser AA, Lee DW, Rajagopalan S, Nicholls DG, Andersen JK & Brand MD. Intrinsic bioenergetic properties and stress-sensitivity of dopaminergic synaptosomes. J. Neurosci. 2011 Mar 23;31(12):4524-34
  14. Birket MJ, Orr AL, Gerencser AA, Madden DT, Vitelli C, Swistowski A, Brand MD, and Zeng X. A reduction in ATP demand and mitochondrial activity with neural differentiation of human embryonic stem cells. Journal of Cell Science, 2011 24:348-58.
  15. Alavez S, Vantipalli MC, Zucker DJ, Klang IM, Lithgow GJ. Amyloid-binding compounds maintain protein homeostasis during ageing and extend lifespan. Nature. 2011 472:226-9
  16. Goehring I, Gerencser AA, Schmidt S, Brand MD, Mulder H, Nicholls DG. Plasma Membrane Potential Oscillations in Insulin Secreting Ins-1 832/13 Cells do not Require Glycolysis and are not Initiated by Fluctuations in Mitochondrial Bioenergetics.  J Biol Chem. 2012 Mar 14.
  17. Gerencser AA, Chinopoulos C, Birket MJ, Jastroch M, Vitelli C, Nicholls DG, Brand MD. Quantitative measurement of mitochondrial membrane potential in cultured cells: calcium-induced de- and hyperpolarization of neuronal mitochondria. J Physiol. 2012 590(Pt 12):2845-71
  18. Kushnareva YE, Gerencser AA, Bossy B, Ju W-K, White a D, Waggoner J, Ellisman MH, Perkins G, Bossy-Wetzel E. Loss of OPA1 disturbs cellular calcium homeostasis and sensitizes for excitotoxicity. Cell Death Differ. 2012 Nov 9;20(2):353–365. PMID: 23138851
  19. Choi SW, Gerencser AA, Ng R, Flynn JM, Melov S, Danielson SR, Gibson BW, Nicholls DG, Bredesen DE, Brand MD. No Consistent Bioenergetic Defects in Presynaptic Nerve Terminals Isolated from Mouse Models of Alzheimer’s Disease. J. Neurosci.  2012 Nov 21;32(47):16775–16784.
  20. Siddiqui A, Chinta SJ, Mallajosyula JK, Rajagopolan S, Hanson I, Rane A, Melov S, Andersen JK. Selective binding of nuclear alpha-synuclein to the PGC1alpha promoter under conditions of oxidative stress may contribute to losses in mitochondrial function: Implications for Parkinson’s disease. Free Radic. Biol. Med. Elsevier; 2012;53(4):993–1003.
  21. Birket MJ, Casini S, Kosmidis G, Elliott DA, Gerencser AA, Baartscheer A, Schumacher C, Mastroberardino PG, Elefanty AG, Stanley EG, Mummery CL.  PGC-1α and Reactive Oxygen Species Regulate Human Embryonic Stem Cell-Derived Cardiomyocyte Function. Stem Cell Reports. 2013 Dec 12;1(6):560-74.
  22. Kawamata H, Ng SK, Diaz N, Burstein S, Morel L, Osgood A, Sider B, Higashimori H, Haydon PG, Manfredi G, Yang Y. Abnormal Intracellular Calcium Signaling and SNARE-Dependent Exocytosis Contributes to SOD1G93AAstrocyte-Mediated Toxicity in Amyotrophic Lateral Sclerosis. J Neurosci. 2014 Feb 5;34(6):2331-48.
  23. Orr AL, Ashok D, Sarantos MR, Ng R, Shi T, Gerencser AA, Hughes RE, Brand MD. Novel Inhibitors of Mitochondrial sn-Glycerol 3-phosphate Dehydrogenase.  PLoS One. 2014 Feb 24;9(2):e89938.
  24. Shaltouki A, Sivapatham R, Pei Y, Gerencser AA, Momčilović O, Rao MS, Zeng X.  Mitochondrial alterations by PARKIN in dopaminergic neurons using PARK2 patient-specific and PARK2 knockout isogenic iPSC lines. Stem Cell Reports. 2015 May 12;4(5):847-59.
  25. Pathak D, Shields L, Mendelsohn BA, Haddad D, Lin W, Gerencser AA, Kim H, Brand MD, Edwards RH, Nakamura K. The Role of Mitochondrially Derived ATP in Synaptic Vesicle Recycling. J Biol Chem. 2015 Sep 11;290(37):22325-36
  26. Gerencser AA. Bioenergetic Analysis of Single Pancreatic Beta-Cells Indicates an Impaired Metabolic Signature in Type 2 Diabetic Subjects. Endocrinology 2015 Oct;156(10):3496-503   Request PDF
  27. Gerencser AA , Mulder H, Nicholls DG. Calcium modulation of exocytosis-linked plasma membrane potential oscillations in INS-1 832/13 cells. Biochem J. 2015 Oct 1;471(1):111-22.
  28. Deng H, Gerencser AA, Jasper H. Signal integration by Ca2+ regulates intestinal stem-cell activity. Nature. 2015 Dec 10;528(7581):212-7
  29. Wiley CD, Velarde MC, Lecot P, Liu S, Sarnoski EA, Freund A, Shirakawa K, Lim HW, Davis SS, Ramanathan A, Gerencser AA, Verdin E, Campisi J. Mitochondrial Dysfunction Induces Senescence with a Distinct Secretory Phenotype. Cell Metab.  doi: 10.1016/j.cmet.2015.11.011.
  30. Doczi J, Torocsik B, Echaniz-Laguna A, Mousson de Camaret B, Starkov A, Starkova N, et al. Alterations in voltage-sensing of the mitochondrial permeability transition pore in ANT1-deficient cells. Sci Rep. 2016;6:26700.
  31. Gerencser AA, Mookerjee SA, Jastroch M, Brand MD. Measurement of the Absolute Magnitude and Time Courses of Mitochondrial Membrane Potential in Primary and Clonal Pancreatic Beta-Cells. PLoS One. 2016;11(7):e0159199.
  32. Brand MD, Goncalves RL, Orr AL, Vargas L, Gerencser AA, Borch Jensen M, Wang YT, Melov S, Turk CN, Matzen JT, Dardov VJ, Petrassi HM, Meeusen SL, Perevoshchikova IV, Jasper H, Brookes PS, Ainscow EK . Suppressors of Superoxide-H2O2 Production at Site IQ of Mitochondrial Complex I Protect against Stem Cell Hyperplasia and Ischemia-Reperfusion Injury. Cell Metab. 2016 Oct 11;24(4):582-592
  33. Németh B, Doczi J, Csete D, Kacso G, Ravasz D, Adams D, Kiss G, Nagy AM, Horvath G, Tretter L, Mócsai A, Csépányi-Kömi R, Iordanov I, Adam-Vizi V, Chinopoulos C. Abolition of mitochondrial substrate-level phosphorylation by itaconic acid produced by LPS-induced Irg1 expression in cells of murine macrophage lineage. FASEB J. 2016 Jan;30(1):286-300.
  34. Carr L, Bardet SM, Burke RC, Arnaud-Cormos D, Leveque P, O'Connor RP. Calcium-independent disruption of microtubule dynamics by nanosecond pulsed electric fields in U87 human glioblastoma cells. Sci Rep. 2017 Jan 24;7:41267
  35. Kabra UD, Pfuhlmann K, Migliorini A, Keipert S, Lamp D, Korsgren O, Gegg M, Woods SC, Pfluger PT, Lickert H, Affourtit C, Tschöp MH, Jastroch M. Direct Substrate Delivery Into Mitochondrial Fission-Deficient Pancreatic Islets Rescues Insulin Secretion. Diabetes. 2017 May;66(5):1247-1257
  36. Carr L, Bardet SM, Arnaud-Cormos D, Leveque P, O'Connor RP Visualisation of an nsPEF induced calcium wave using the genetically encoded calcium indicator GCaMP in U87 human glioblastoma cells. Bioelectrochemistry. 2017 Sep 8;119:68-75
  37. Burke RC, Bardet SM, Carr L, Romanenko S, Arnaud-Cormos D, Leveque P, O'Connor RP. Nanosecond pulsed electric fields depolarize transmembrane potential via voltage-gated K+, Ca2+ and TRPM8 channels in U87 glioblastoma cells. Biochim Biophys Acta. 2017 Oct;1859(10):2040-2050.
  38. Debattisti V, Gerencser AA, Saotome M, Das S, Hajnóczky G. ROS Control Mitochondrial Motility through p38 and the Motor Adaptor Miro/Trak. Cell Rep. 2017 Nov 7;21(6):1667-1680.
  39. Liao EH, Gray L, Tsurudome K, El-Mounzer W, Elazzouzi F, Baim C, Farzin S, Calderon MR, Kauwe G, Haghighi AP. Kinesin Khc-73/KIF13B modulates retrograde BMP signaling by influencing endosomal dynamics at the Drosophila neuromuscular junction. PLoS Genet. 2018 Jan 26;14(1):e1007184
  40. Guntur AR, Gerencser AA, Le PT, DeMambro VE, Bornstein SA, Mookerjee SA, Maridas DE, Clemmons DE, Brand MD, Rosen CJ. Osteoblast-like MC3T3-E1 Cells Prefer Glycolysis for ATP Production but Adipocyte-like 3T3-L1 Cells Prefer Oxidative Phosphorylation. J Bone Miner Res. 2018 Jun;33(6):1052–1065
  41. Gerencser AA. Metabolic activation-driven mitochondrial hyperpolarization predicts insulin secretion in human pancreatic beta-cells. Biochim Biophys Acta Bioenerg. 2018 Sep;1859(9):817-828
  42. Peters TW, Nelson CS, Gerencser AA, Dumas KJ, Tavshanjian B, Chang KC, Lithgow GJ, Hughes RE. Natural Genetic Variation in Yeast Reveals That NEDD4 Is a Conserved Modifier of Mutant Polyglutamine Aggregation. G3 (Bethesda). 2018 Nov 6;8(11):3421-3431
  43. Svab G, Doczi J, Gerencser AA, Ambrus A, Gallyas F, Sümegi B, Tretter L. The Mitochondrial Targets of Neuroprotective Drug Vinpocetine on Primary Neuron Cultures, Brain Capillary Endothelial Cells, Synaptosomes, and Brain Mitochondria. Neurochem Res. 2019 Oct;44(10):2435-2447
  44. Sasikumar AN, Killilea DW, Kennedy BK, Brem RB. Potassium restriction boosts vacuolar acidity and extends lifespan in yeast. Exp Gerontol. 2019 Jun;120:101-106
  45. Taibi A, Albouys J, Jacques J, Perrin M-L, Yardin C, Durand Fontanier S, Bardet SM. Comparison of implantation sites for the development of peritoneal metastasis in a colorectal cancer mouse model using non-invasive bioluminescence imaging. PLoS One. 2019 Jul 31;14(7):e0220360.
  46. Wong HS, Mezera V, Dighe P, Melov S, Gerencser AA, Sweis RF, Pliushchev M, Wang Z, Esbenshade T, McKibben B, Riedmaier S, Brand MD. Superoxide produced by mitochondrial site IQ inactivates cardiac succinate dehydrogenase and induces hepatic steatosis in Sod2 knockout mice. Free Radic Biol Med . 2021 Feb 20;164:223-232
  47. Dijk G, Ruigrok HJ, O’Connor RP. Influence of PEDOT:PSS Coating Thickness on the Performance of Stimulation Electrodes. Adv Mater Interfaces. 2020 Aug 22;7(16):2000675.
  48. Morris O, Deng H, Tam C, Jasper H. Warburg-like Metabolic Reprogramming in Aging Intestinal Stem Cells Contributes to Tissue Hyperplasia. Cell Rep. 2020 Nov;33(8):108423.
  49. Louie MC, Ton J, Brady ML, Le DT, Mar JN, Lerner CA, Gerencser AA, Mookerjee SA. Total Cellular ATP Production Changes With Primary Substrate in MCF7 Breast Cancer Cells. Front Oncol. 2020;10(November):1–12
  50. Namba T, Dóczi J, Pinson A, Xing L, Kalebic N, Wilsch-Bräuninger M, Long KR, Vaid S, Lauer J, Bogdanova A, Borgonovo B, Shevchenko A, Keller P, Drechsel D, Kurzchalia T, Wimberger P, Chinopoulos C, Huttner WB. Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis. Neuron. 2020;105(5):867-881.e9.
  51. Rovini A, Heslop K, Hunt EG, Morris ME, Fang D, Gooz M, Gerencser AA, Maldonado EN. Quantitative analysis of mitochondrial membrane potential heterogeneity in unsynchronized and synchronized cancer cells. FASEB J. 2021 Jan 16;35(1):100–106.
  52. Orlacchio R, Carr L, Palego C, Arnaud-Cormos D, Leveque P. High-voltage 10 ns delayed paired or bipolar pulses for in vitro bioelectric experiments. Bioelectrochemistry 2021 Feb;137:107648.
  53. Angeli S, Foulger A, Chamoli M, Peiris TH, Gerencser A, Shahmirzadi AA, Andersen J, Lithgow G. The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging. Elife. 2021 Sep 1;10:2020.11.03.366815.
  54. Carr L, Golzio M, Orlacchio R, Alberola G, Kolosnjaj-Tabi J, Leveque P, Arnaud-Cormos D, Rols M-P. A nanosecond pulsed electric field (nsPEF) can affect membrane permeabilization and cellular viability in a 3D spheroids tumor model. Bioelectrochemistry. 2021 Oct;141:107839.
  55. Puchkov E. Image analysis in microbiology: a review. Journal of Computer and Communications. 2016;4(15):8.
  56. Dijk G, Ruigrok HJ, O'Connor RP. PEDOT: PSS‐Coated Stimulation Electrodes Attenuate Irreversible Electrochemical Events and Reduce Cell Electropermeabilization. Advanced Materials Interfaces. 21;8(19):2100214.
  57. Lim Y, Cho IT, Rennke HG, Cho G. beta2-adrenergic receptor regulates ER-mitochondria contacts. Sci Rep. 21;11(1):21477.
  58. Orlacchio R, Carr L, Palego C, Arnaud-Cormos D, Leveque P. High-voltage 10 ns delayed paired or bipolar pulses for in vitro bioelectric experiments. Bioelectrochemistry. 2021;137:107648.
  59. Wong HS, Mezera V, Dighe P, Melov S, Gerencser AA, Sweis RF, Pliushchev M, Wang Z, Esbenshade T, McKibben B, Riedmaier S, Brand MD. Superoxide produced by mitochondrial site IQ inactivates cardiac succinate dehydrogenase and induces hepatic steatosis in Sod2 knockout mice. Free Radic Biol Med. 2021;164:223-32.
  60. Dijk G, Poulkouras R, RP OC. Electroporation Microchip With Integrated Conducting Polymer Electrode Array for Highly Sensitive Impedance Measurement. IEEE Trans Biomed Eng. 2022;69(7):2363-9.
  61. Lerner CA, Gerencser AA. Unbiased Millivolts Assay of Mitochondrial Membrane Potential in Intact Cells. In: Tomar N, editor. Mitochondria. Methods in Molecular Biology. New York, NY: Humana. p. 11-61.
  62. Poulkouras R, Dijk G, Lefevre M, Baca M, Moreau D, O'Connor RP. PEDOT:PSS coated electrodes reduce intracellular oxidation and cell damage with pulsed electric field application. Bioelectrochemistry. 2022;147:108163.
  63. Chamoli M, Rane A, Chinta S, Shahmirzadi A, Kumsta C, Nambiar D, Hall D, Foulger A, Angeli S, Schmidt M, Pitteri S, Hansen M, Lithgow G, Andersen J. A drug-like molecule engages a nuclear hormone receptor to regulate mitophagy and promote mitochondrial mediated lifespan 2022.
  64. Doczi J, Karnok N, Bui D, Azarov V, Pallag G, Nazarian S, Czumbel B, Seyfried TN, Chinopoulos C. Viability of HepG2 and MCF-7 Cells is not Correlated with Mitochondrial Bioenergetics 2022 doi: 10.1101/2022.12.01.518661.
  65. Tshilenge KT , Aguirre CG, Bons J, Gerencser AA, Basisty N, Song S, Rose J, Lopez-Ramirez A, Naphade S, Loureiro A, Battistoni E, Milani M, Wehrfritz C, Holtz A, Hetz C, Mooney SD, Schilling B, Ellerby LM. Proteomic Analysis of Huntington's Disease Medium Spiny Neurons Identifies Alterations in Lipid Droplets. Mol Cell Proteomics. 2023;22(5):100534.
  66. Neri F , Takajjart NS, Lerner AC, Desprez P, Schilling B, Campisi J, Gerencser AA. A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers. BIORXIV/2023/573123