Wound Healing Tool

The MRI Wound Healing Tool can be used to analyze scratch assays. It measures the area of a wound in a cellular tissue on a stack of images representing a time-series. An example image can be found here. An example image for the find-edges method (see below) can be found here.

Getting Started

To install the tools, drag the link MRI_Wound_Healing_Tool.ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the "MRI Wound Healing Tool" toolset from the >> button of the ImageJ launcher.

  • the first button opens this help-page.
  • the m button starts the measurement on the active stack

Options

By right-clicking on the m button you can open the options dialog.

  • method: You can choose between a variance based method and a method based on find edges. Note that for find edges the parameters variance-filter-radius and threshold are not taken into account.
  • variance filter radius: The radius of the variance filter that is applied to separate the zone occupied by tissue from the empty zone. The radius must be big enough so that the variance due to the tissue plays a role compared to the variance of the noise in the image. Note that the calculation time becomes longer with a bigger radius.
  • threshold The image resulting from the variance filter is converted to a mask by applying the given threshold. If the input images are 16bit the threshold 1 will probably work.
  • radius open This operation will close holes in the tissue. It must be big enough to close small holes in the tissue and small enough to not close the area of the wound in later images.
  • min. size Minimum size from which on the wound is taken into account. This excludes small remaining holes in the tissue.
  • ignore spatial calibration If checked the measurements will be in pixel otherwise the spatial calibration of the image if any is used.

Hints

  • In ImageJ, select Analyze>Set Measurements to select the features you want to measure. You should at least select area and Display label.
  • It can happen that the result at one time-point consists of more then one area. You can recognize it because they have the same number in the column slice of the results table. To get the total area for one time-point you need to add all the surfaces measured for that time-point
  • Make sure that the option Black background is set in dialog accesible via the menu Process>Binary>options.... Without this option the tool will not work correctly.

Results

See also

Publications using this tool

  1. Lundby, A., Franciosa, G., Emdal, K.B., Refsgaard, J.C., Gnosa, S.P., Bekker-Jensen, D.B., Secher, A., Maurya, S.R., Paul, I., Mendez, B.L., et al. (2019). Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites. Cell 179, 543-560.e26.
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  2. Davis, J.B., Krishna, S.S., Abi Jomaa, R., Duong, C.T., Espina, V., Liotta, L.A., and Mueller, C. (2019). A new model isolates glioblastoma clonal interactions and reveals unexpected modes for regulating motility, proliferation, and drug resistance. Sci Rep 9, 17380.
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  3. Pavlovic, N., Thanapirom, K., Mazza, G., Rombouts, K., Gerwins, P., and Heindryckx, F. (2019). Blocking IRE1a;-endoribonuclease activity in hepatic stellate cells decreases tumor cell proliferation and metastasis in hepatocellular carcinoma (Cancer Biology).
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  4. Michel, M., Hollenbach, M., Pohl, S., Ripoll, C., and Zipprich, A. (2019). Inhibition of Glyoxalase-I Leads to Reduced Proliferation, Migration and Colony Formation, and Enhanced Susceptibility to Sorafenib in Hepatocellular Carcinoma. Front. Oncol. 9, 785.
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  5. Yasi, E.A., Allen, A.A., Sugianto, W., and Peralta-Yahya, P. (2019). Identification of Three Antimicrobials Activating Serotonin Receptor 4 in Colon Cells. ACS Synth. Biol. acssynbio.9b00310.
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  6. Marzoq, A.J., Mustafa, S.A., Heidrich, L., Hoheisel, J.D., and Alhamdani, M.S.S. (2019). Impact of the secretome of activated pancreatic stellate cells on growth and differentiation of pancreatic tumour cells. Sci Rep 9, 5303.
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  7. Schäfer, A., Gjerga, E., Welford, R.W., Renz, I., Lehembre, F., Groenen, P.M., Saez‐Rodriguez, J., Aebersold, R., and Gstaiger, M. (2019). Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data. Mol Syst Biol 15.
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  8. Venturi, G., Gomes Ferreira, I., Pucci, M., Ferracin, M., Malagolini, N., Chiricolo, M., and Dall’Olio, F. (2019). Impact of sialyltransferase ST6GAL1 overexpression on different colon cancer cell types. Glycobiology 29, 684–695.
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  9. Fang, L.-W., Kao, Y.-H., Chuang, Y.-T., Huang, H.-L., and Tai, T.-S. (2019). Ets-1 enhances tumor migration through regulation of CCR7 expression. BMB Rep. 52, 548–553.
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  10. Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., and Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Sci Rep 9, 12625.
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  11. Abdallah, S., Abu-Reidah, I., Mousa, A., and Abdel-Latif, T. (2019). Rhus coriaria (sumac) extract reduces migration capacity of uterus cervix cancer cells. Revista Brasileira de Farmacognosia S0102695X19300547.
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  12. Yagnik, G., Rutowski, M.J., Shah, S.S., and Aghi, M.K. (2019). Stratifying nonfunctional pituitary adenomas into two groups distinguished by macrophage subtypes. Oncotarget 10.
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  13. Bashari, M.H., Huda, F., Tartila, T.S., Shabrina, S., Putri, T., Qomarilla, N., Atmaja, H., Subhan, B., Sudji, I.R., and Meiyanto, E. (2019). Bioactive Compounds in the Ethanol Extract of Marine Sponge Stylissa carteri Demonstrates Potential Anti-Cancer Activity in Breast Cancer Cells. Asian Pac J Cancer Prev 20, 1199–1206.
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  14. Stafman, L.L., Waldrop, M.G., Williams, A.P., Aye, J.M., Stewart, J.E., Mroczek-Musulman, E., Yoon, K.J., Whelan, K., and Beierle, E.A. (2019). The Presence of PIM3 Increases Hepatoblastoma Tumorigenesis and Tumor Initiating Cell Phenotype and is Associated with Decreased Patient Survival. Journal of Pediatric Surgery.
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  15. Schacke, M., Kumar, J., Colwell, N., Hermanson, K., Folle, G., Nechaev, S., Dhasarathy, A., and Lafon-Hughes, L. (2019). PARP-1/2 Inhibitor Olaparib Prevents or Partially Reverts EMT Induced by TGF-β in NMuMG Cells. International Journal of Molecular Sciences 20, 518.
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  16. Brissos, R.F., Clavero, P., Gallen, A., Grabulosa, A., Barrios, L.A., Caballero, A.B., Korrodi-Gregório, L., Pérez-Tomás, R., Muller, G., Soto-Cerrato, V., et al. (2018). Highly Cytotoxic Ruthenium(II)-Arene Complexes from Bulky 1-Pyrenylphosphane Ligands. Inorg. Chem. 57, 14786–14797.
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  17. Lasiste, J.M., Zoroquiain, P., Miyamoto, D., and Burnier, M. (2018). Metformin activity in an in vitro model of posterior capsule opacification. Vision Pan-America, The Pan-American Journal of Ophthalmology 17, 105–112.
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  18. Jessica Warrington (2018). The Role of Receptor Activity Modifying Protein 1 in Prostate Cancer. PhD thesis. University of Sheffield.
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  19. Asiri, A., Toss, M.S., Raposo, T.P., Akhlaq, M., Thorpe, H., Alfahed, A., Asiri, A., and Ilyas, M. (2018). The Cten signalling pathway stabilises Src protein to promote Epithelial-Mesenchymal Transition (EMT) in colorectal cancer. BioRxiv.
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  20. Anne Lewis Carlton (2018). The role of CBFβ in ovarian cancer. University of Virginia.
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  21. Walerych, D., Pruszko, M., Zyla, L., Wezyk, M., Gaweda-Walerych, K., and Zylicz, A. (2018). Wild-type p53 oligomerizes more efficiently than p53 hot-spot mutants and overcomes mutant p53 gain-of-function via a "dominant-positive" mechanism. Oncotarget 9.
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  22. Accornero, P., Martignani, E., Miretti, S., and Baratta, M. (2018). Murine and Human Mammary Cancer Cell Lines: Functional Tests. In Epithelial Cell Culture, M. Baratta, ed. (New York, NY: Springer New York), pp. 169–183.
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  23. Daniel, B., Nagy, G., Czimmerer, Z., Horvath, A., Hammers, D.W., Cuaranta-Monroy, I., Poliska, S., Tzerpos, P., Kolostyak, Z., Hays, T.T., et al. (2018). The Nuclear Receptor PPARγ Controls Progressive Macrophage Polarization as a Ligand-Insensitive Epigenomic Ratchet of Transcriptional Memory. Immunity 49, 615-626.e6.
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  24. Carlton, A.L., Illendula, A., Gao, Y., Llaneza, D.C., Boulton, A., Shah, A., Rajewski, R.A., Landen, C.N., Wotton, D., and Bushweller, J.H. (2018). Small molecule inhibition of the CBFβ/RUNX interaction decreases ovarian cancer growth and migration through alterations in genes related to epithelial-to-mesenchymal transition. Gynecologic Oncology 149, 350–360.
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  25. Stamm, A., Strauß, S., Vogt, P., Scheper, T., and Pepelanova, I. (2018). Positive in vitro wound healing effects of functional inclusion bodies of a lipoxygenase from the Mexican axolotl. Microbial Cell Factories 17.
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  26. Berning, P., Schaefer, C., Clemens, D., Korsching, E., Dirksen, U., and Potratz, J. (2018). The CXCR4 antagonist plerixafor (AMD3100) promotes proliferation of Ewing sarcoma cell lines in vitro and activates receptor tyrosine kinase signaling. Cell Communication and Signaling 16.
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  27. Prestigiacomo, V., and Suter-Dick, L. (2018). Nrf2 protects stellate cells from Smad-dependent cell activation. PLOS ONE 13, e0201044.
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  28. Leifheit-Nestler, M., Kirchhoff, F., Nespor, J., Richter, B., Soetje, B., Klintschar, M., Heineke, J., and Haffner, D. (2018). Fibroblast growth factor 23 is induced by an activated renin–angiotensin–aldosterone system in cardiac myocytes and promotes the pro-fibrotic crosstalk between cardiac myocytes and fibroblasts. Nephrology Dialysis Transplantation, 33, 1722–1734.
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  29. Hopkins, B.L., Nadler, M., Skoko, J.J., Bertomeu, T., Pelosi, A., Shafaei, P.M., Levine, K., Schempf, A., Pennarun, B., Yang, B., et al. (2018). A Peroxidase Peroxiredoxin 1-Specific Redox Regulation of the Novel FOXO3 microRNA Target let-7. Antioxidants & Redox Signaling 28, 62–77.
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  30. Saini, M., Verma, A., and Mathew, S.J. (2018). SPRY2 is a novel MET interactor that regulates metastatic potential and differentiation in rhabdomyosarcoma. Cell Death & Disease 9.
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  31. Fung, E., Richter, C., Yang, H., Schäffer, I., Fischer, R., Kessler, B.M., Bassermann, F., and D’Angiolella, V. (2018). FBXL13 directs the proteolysis of CEP192 to regulate centrosome homeostasis and cell migration. EMBO Reports e44799.
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  32. Hauck, P.M., Wolf, E.R., Olivos, D.J., Batuello, C.N., McElyea, K.C., McAtarsney, C.P., Cournoyer, R.M., Sandusky, G.E., and Mayo, L.D. (2017). Early-Stage Metastasis Requires Mdm2 and Not p53 Gain of Function. Molecular Cancer Research 15, 1598–1607.
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  33. Sun, X., Wang, S.C., Wei, Y., Luo, X., Jia, Y., Li, L., Gopal, P., Zhu, M., Nassour, I., Chuang, J.-C., et al. (2017). Arid1a Has Context-Dependent Oncogenic and Tumor Suppressor Functions in Liver Cancer. Cancer Cell 32, 574–589.e6.
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  34. Castañón, E., Soltermann, A., López, I., Román, M., Ecay, M., Collantes, M., Redrado, M., Baraibar, I., López-Picazo, J.M., Rolfo, C., et al. (2017). The inhibitor of differentiation-1 ( Id1 ) enables lung cancer liver colonization through activation of an EMT program in tumor cells and establishment of the pre-metastatic niche. Cancer Letters 402, 43–51.
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  35. Jade Marie Edenvirg Fontanilla Lasiste (2017). METFORMIN INHIBITS EPITHELIAL-TO-MESENCHYMAL TRANSITION IN LENS EPITHELIAL CELLS. Master of Science (MSc) in Pathology. McGill University.
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  36. Hauck, P.M., Wolf, E.R., Olivos, D.J., Batuello, C.N., McElyea, K.C., McAtarsney, C.P., Cournoyer, R.M., Sandusky, G.E., and Mayo, L.D. (2017). Early-Stage Metastasis Requires Mdm2 and Not p53 Gain of Function. Molecular Cancer Research 15, 1598–1607.
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  37. Duanduan Cong (2017). Identification of functional single nucleotide polymorphisms (SNPs) in High Risk-Human Papillomavirus (HR-HPV) related diseases. The University of Edinburgh.
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  38. Auer, S., Rinnerthaler, M., Bischof, J., Streubel, M.K., Breitenbach-Koller, H., Geisberger, R., Aigner, E., Cadamuro, J., Richter, K., Sopjani, M., et al. (2017). The Human NADPH Oxidase, Nox4, Regulates Cytoskeletal Organization in Two Cancer Cell Lines, HepG2 and SH-SY5Y. Frontiers in Oncology 7.
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  39. Kabała-Dzik, A., Rzepecka-Stojko, A., Kubina, R., Jastrzębska-Stojko, Ż., Stojko, R., Wojtyczka, R., and Stojko, J. (2017). Migration Rate Inhibition of Breast Cancer Cells Treated by Caffeic Acid and Caffeic Acid Phenethyl Ester: An In Vitro Comparison Study. Nutrients 9, 1144.
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  40. Juneja, M., Kobelt, D., Walther, W., Voss, C., Smith, J., Specker, E., Neuenschwander, M., Gohlke, B.-O., Dahlmann, M., Radetzki, S., et al. (2017). Statin and rottlerin small-molecule inhibitors restrict colon cancer progression and metastasis via MACC1. PLOS Biology 15, e2000784.
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  41. Morry, J., Ngamcherdtrakul, W., Gu, S., Reda, M., Castro, D.J., Sangvanich, T., Gray, J.W., and Yantasee, W. (2017). Targeted Treatment of Metastatic Breast Cancer by PLK1 siRNA Delivered by an Antioxidant Nanoparticle Platform. Molecular Cancer Therapeutics 16, 763–772.
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  42. Qiao, Y., Chen, J., Lim, Y.B., Finch-Edmondson, M.L., Seshachalam, V.P., Qin, L., Jiang, T., Low, B.C., Singh, H., Lim, C.T., et al. (2017). YAP Regulates Actin Dynamics through ARHGAP29 and Promotes Metastasis. Cell Reports 19, 1495–1502.
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  43. Mahendra, A., Yang, X., Abnouf, S., Park, D., Soomro, S., Adolacion, J.R.T., Roszik, J., Coarfa, C., Romain, G., Wanzeck, K., et al. (2017). Beyond Autoantibodies: Biological Roles Of Human Autoreactive B Cells In Rheumatoid Arthritis Revealed By Whole Transcriptome Profiling. preprint
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  44. Ottosson, M., Jakobsson, A., and Johansson, F. (2017). Accelerated Wound Closure - Differently Organized Nanofibers Affect Cell Migration and Hence the Closure of Artificial Wounds in a Cell Based In Vitro Model.
    PLOS ONE 12, e0169419.
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  45. Buesch, S., Schaepermeier, S., D’Souza, T., Ortmann, B., Schwartz, C., and Schroeder, J. (2017). Abstract 822: Simple and easy monitoring of tube formation and migration assays with the CytoSMART TM Live Cell Imaging System. Cancer Research 77, 822–822. See also this poster
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  46. Walter, Thomas M. & Merish, S. (2016). In-Vitro wound healing activity of Herbal topical formulation on H9C2 Heart cells. Siddha Papers 0974-2522. 2016(1). 1-11.
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  47. Saenz-de-Viteri, M., Fernández-Robredo, P., Hernández, M., Bezunartea, J., Reiter, N., Recalde, S., and García-Layana, A. (2016). Single- and repeated-dose toxicity study of bevacizumab, ranibizumab, and aflibercept in ARPE-19 cells under normal and oxidative stress conditions. Biochemical Pharmacology 103, 129–139.
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  48. Yong, L.-K., Lai, S., Liang, Z., Poteet, E., Chen, F., van Buren, G., Fisher, W., Mo, Q., Chen, C., and Yao, Q. (2016). Overexpression of Semaphorin-3E enhances pancreatic cancer cell growth and associates with poor patient survival. Oncotarget 7.
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  49. Urello, M.A., Kiick, K.L., and Sullivan, M.O. (2016). Integration of growth factor gene delivery with collagen-triggered wound repair cascades using collagen-mimetic peptides. Urello et al. Bioengineering & Translational Medicine 1, 207–219.
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  50. Bissonnette, L., Drissennek, L., Antoine, Y., Tiers, L., Hirtz, C., Lehmann, S., Perrochia, H., Bissonnette, F., Kadoch, I.-J., Haouzi, D., et al. (2016). Human S100A10 plays a crucial role in the acquisition of the endometrial receptivity phenotype. Cell Adhesion & Migration 10, 282–298.
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  51. Alvarado-Ruiz, L., Martinez-Silva, M.G., Torres-Reyes, L.A., Pina-Sanchez, P., Ortiz-Lazareno, P., Bravo-Cuellar, A., Aguilar-Lemarroy, A., and Jave-Suarez, L.F. (2016). HOXA9 is Underexpressed in Cervical Cancer Cells and its Restoration Decreases Proliferation, Migration and Expression of Epithelial-to-Mesenchymal Transition Genes. Asian Pacific Journal of Cancer Prevention 17, 1037–1047.
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  52. Zhang, R.-Y., Yu, Z.-H., Zeng, L., Zhang, S., Bai, Y., Miao, J., Chen, L., Xie, J., and Zhang, Z.-Y. (2016). SHP2 phosphatase as a novel therapeutic target for melanoma treatment. Oncotarget.
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  53. Cormier, N., Yeo, A., Fiorentino, E., and Paxson, J. (2015). Optimization of the Wound Scratch Assay to Detect Changes in Murine Mesenchymal Stromal Cell Migration After Damage by Soluble Cigarette Smoke Extract. Journal of Visualized Experiments.
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  54. Leach, D.A., Need, E.F., Toivanen, R., Trotta, A.P., Palenthorpe, H.M., Tamblyn, D.J., Kopsaftis, T., England, G.M., Smith, E., Drew, P.A., et al. (2015). Stromal androgen receptor regulates the composition of the microenvironment to influence prostate cancer outcome. Oncotarget 6, 16135–16150.
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  55. Nathalia S. Laszkiewicz, Graziela G. Romagnoli, Carolina M. Gorgulho, Ethel
    Cesarman, Ramon Kaneno, Deilson E. Oliveira. In vitro migration and cellular invasion of human cells expressing variants of the Epstein-Barr virus LMP1 oncoprotein. In Nathália Suiti Laszkiewicz (2015). Migração e invasão celular in vitro de células humanas expressando variantes da proteína LMP1 do vírus de Epstein-Barr. Mestre em Patologia. UNIVERSIDADE ESTADUAL PAULISTA “JÚLIO DE MESQUITA FILHO.”
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  56. Sánchez-Bailón, M.P., Calcabrini, A., Mayoral-Varo, V., Molinari, A., Wagner, K.-U., Losada, J.P., Ciordia, S., Albar, J.P., and Martín-Pérez, J. (2015). Cyr61 as mediator of Src signaling in triple negative breast cancer cells. Oncotarget 6, 13520–13538.
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  57. Sushobhna Batra, Richard A. Rabin
    Poster: Effects of Ethanol on Brain Injury: Role of Microglial Migration
    2015, University at Buffalo

Other references

  1. Palacio, J., Johanna, L., n, G., Pablo, J., Carolina, D., and Carlos, J. ENSAYO DE CICATRIZACIÓN IN VITRO, PARA EVALUAR MIGRACIÓN CELULAR v2 (protocols.io.kdics4e).
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  2. Protocolo de ENSAYO DE HERIDA (Spanish), Universidad Autonoma de Madrid, 2013

Wound_Healing-Tool.png (497 Bytes) Volker Baecker, 11/16/2011 02:16 PM

wound_healing.tif - test input file with only 3 time-points to keep the size small (74.5 MB) Volker Baecker, 11/16/2011 03:34 PM

wound-healing-res01.png (137 KB) Volker Baecker, 11/16/2011 03:49 PM

wound-healing-res02.png (141 KB) Volker Baecker, 11/16/2011 03:50 PM

wound-healing-res03.png (1.83 KB) Volker Baecker, 11/16/2011 03:50 PM

Wound_Healing_Tool_Options.png (7.43 KB) Volker Baecker, 02/23/2012 01:28 PM

t_003.tif (13.9 MB) Volker Baecker, 02/23/2012 01:33 PM

wound_healing_options.png (9.78 KB) Volker Baecker, 06/01/2017 11:48 AM