MRI_Fibrosis_Tool - MontpellierRessourcesImagerie/imagej_macros_and_scripts GitHub Wiki

MRI Fibrosis Tool

Measure the relative area of sirius red stained fibrosis. The tool uses the colour deconvolution plugin from Gabriel Landini.

You can find test images here and here.

Getting started

To install the tool, drag the link MRI_Fibrosis_Tool.ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation.

Select the "MRI_Fibrosis_Tool" toolset from the >> button of the ImageJ launcher.

fibrosis-toolset.png

  • the first button (the one with the image) opens this help page.
  • the m-button runs the analysis on the active window. Note that you should crop the image and that there should be a selection (roi) on the cropped image.
  • the b-button runs the analysis on a folder containing cropped images with a selection (roi) in tif-format.

Options

Right-click on the m-button to open the general options dialog:

general-options.png

  • r1, g1, b1 - the RGB-components (between 0 and 1) of the colour we want to segment.
  • r2, g2, b2 - the RGB-components (between 0 and 1) of the first background colour.
  • r3, g3, b3 - the RGB-components (between 0 and 1) of the second background colour.
  • file ext. - the file extension (including the dot) of the input files

Right-click on the b-button to open the batch-options dialog:

Batch-options.png

  • control folder - the name of the sub-folder into which the control images will be saved
  • results table - the name of the results table and the results spreadsheet file (csv text saved as .xls)

Method

Colour deconvolution is used to separate the staining into a single image. A simple auto-threshold with the default method is applied and a selection is created. The area of the selection is measured and compared to the area of the selection on the input image. The colour deconvolution is done using the Colour Deconvolution Plugin1 from Gabriel Landini

Note that you can use the colour deconvolution plugin if you need to find different colour vectors. You can then enter the new values in the options dialog or change the default values in the macro's source code.

1: ImageJ.net - Colour Deconvolution

Results

input01.png result01.png input02.png result02.png result-measurements.png |

Publications using the tool

  1. Osorio-Conles, Ó., Ibarzabal, A., Balibrea, J.M., Vidal, J., Ortega, E., and De Hollanda, A. (2023). FABP4 Expression in Subcutaneous Adipose Tissue Is Independently Associated with Circulating Triglycerides in Obesity. JCM 12, 1013. 10.3390/jcm12031013.

  2. Osorio-Conles, Ó., Jiménez, A., Ibarzabal, A., Balibrea, J.M., De Hollanda, A., and Vidal, J. (2023). Limited Bariatric Surgery-induced Weight Loss in Subjects With Type 2 Diabetes: Predictor Variables in Adipose Tissue. The Journal of Clinical Endocrinology & Metabolism 108, e1205–e1213. 10.1210/clinem/dgad271.

  3. Grillet, P.-E., Desplanche, E., Wynands, Q., Gouzi, F., Bideaux, P., Fort, A., Scheuermann, V., Lacampagne, A., Virsolvy, A., Thireau, J., et al. (2023). Diastolic Cardiomyopathy Secondary to Experimentally Induced Exacerbated Emphysema. Am J Respir Cell Mol Biol 69, 230–241. 10.1165/rcmb.2022-0382OC.

  4. Matias, G.S.S., Carreira, A.C.O., Batista, V.F., Barreto, R.S.N., Miglino, M.A., and Fratini, P. (2023). Ionic Detergent Under Pressure-Vacuum as an Innovative Strategy to Generate Canine Tracheal Scaffold for Organ Engineering. Cells Tissues Organs 212, 535–545. 10.1159/000525273.

  5. Osorio-Conles, Ó., Olbeyra, R., Vidal, J., Ibarzabal, A., Balibrea, J.M., and De Hollanda, A. (2023). Expression of Adipose Tissue Extracellular Matrix-Related Genes Predicts Weight Loss after Bariatric Surgery. Cells 12, 1262. 10.3390/cells12091262.

  6. Kruppa, P., Gohlke, S., Łapiński, K., Garcia-Carrizo, F., Soultoukis, G.A., Infanger, M., Schulz, T.J., and Ghods, M. (2023). Lipedema stage affects adipocyte hypertrophy, subcutaneous adipose tissue inflammation and interstitial fibrosis. Front. Immunol. 14, 1223264. 10.3389/fimmu.2023.1223264.

  7. Krehl, K., Hahndorf, J., Stolzenburg, N., Taupitz, M., Braun, J., Sack, I., Schnorr, J., and Guo, J. (2023). Characterization of renal fibrosis in rats with chronic kidney disease by in vivo tomoelastography. NMR in Biomedicine, e5003. 10.1002/nbm.5003.

  8. Rojo‐García, A.V., Vanmunster, M., Pacolet, A., and Suhr, F. (2023). Physical inactivity by tail suspension alters markers of metabolism, structure, and autophagy of the mouse heart. Physiological Reports 11. 10.14814/phy2.15574.

  9. Wertheim, B. M. et al. Proline and glucose metabolic reprogramming supports vascular endothelial and medial biomass in pulmonary arterial hypertension. JCI Insight (2023) doi:10.1172/jci.insight.163932.

  10. Boissière‑Michot, F., Mollevi, C., Baecker, V., Crapez, E., Jacot, W., 2022. In situ hybridization for the assessment of urokinase plasminogen activator and plasminogen activator inhibitor type‑1 in formalin‑fixed paraffin‑embedded breast cancer specimens. Int J Mol Med 49, 82. https://doi.org/10.3892/ijmm.2022.5138

  11. Benjamin Englert (2022). The Role of Stromal Hedgehog Signaling in Intestinal Fibrosis of Mice. Universitätsmedizin Berlin.

  12. Alle, Q., Le Borgne, E., Bensadoun, P., Lemey, C., Béchir, N., Gabanou, M., Estermann, F., Bertrand‐Gaday, C., Pessemesse, L., Toupet, K., et al. (2022). A single short reprogramming early in life initiates and propagates an epigenetically related mechanism improving fitness and promoting an increased healthy lifespan. Aging Cell 21. 10.1111/acel.13714.

  13. Chaiyadet, S., Tangkawattana, S., Smout, M.J., Ittiprasert, W., Mann, V.H., Deenonpoe, R., Arunsan, P., Loukas, A., Brindley, P.J., and Laha, T. (2022). Knockout of liver fluke granulin, Ov-grn-1, impedes malignant transformation during chronic infection with Opisthorchis viverrini. PLoS Pathog 18, e1010839. 10.1371/journal.ppat.1010839.

  14. Balzer, M.S., Doke, T., Yang, Y.-W., Aldridge, D.L., Hu, H., Mai, H., Mukhi, D., Ma, Z., Shrestha, R., Palmer, M.B., et al. (2022). Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nat Commun 13, 4018.

  15. Nguyen, A.V., Bagood, M.D., Wang, M., Caryotakis, S.E., Smith, G., Yee, S., Shen, H., Isseroff, R.R., and Soulika, A.M. (2022). Montelukast, an Antagonist of Cysteinyl Leukotriene Signaling, Impairs Burn Wound Healing. Plastic & Reconstructive Surgery 150, 92e–104e. 10.1097/PRS.0000000000009228.

  16. Enora LE BORGNE (2022). Reprogrammation cellulaire pour améliorer la régénération tissulaire altérée dans les pathologies du vieillissement.

  17. Gasmi, I., Machou, C., Rodrigues, A., Brouillet, A., Nguyen, T.C., Rousseau, B., Guillot, A., Rodriguez, C., Demontant, V., Ait-Ahmed, Y., Calderaro, J., Luciani, A., Pawlotsky, J.-M., Lafdil, F., 2022. Interleukin-17 programs liver progenitor cell transformation into cancer stem cells through mir-122 downregulation with increased risk of primary liver cancer initiation. Int. J. Biol. Sci. 18, 1944–1960. https://doi.org/10.7150/ijbs.70408

  18. Osorio-Conles, Ó., Vega-Beyhart, A., Ibarzabal, A., Balibrea, J.M., Vidal, J., de Hollanda, A., 2022. Biological Determinants of Metabolic Syndrome in Visceral and Subcutaneous Adipose Tissue from Severely Obese Women. IJMS 23, 2394. https://doi.org/10.3390/ijms23042394

  19. Kobayashi, H. et al. The Balance of Stromal BMP Signaling Mediated by GREM1 and ISLR Drives Colorectal Carcinogenesis. Gastroenterology 160, 1224-1239.e30 (2021).

  20. Tarasenko, N. et al. (2021) Valproic Acid Prodrug Affects Selective Markers, Augments Doxorubicin Anticancer Activity and Attenuates Its Toxicity in a Murine Model of Aggressive Breast Cancer, Pharmaceuticals, 14(12), p. 1244. doi:10.3390/ph14121244.

  21. de Bakker, D.E.M., Bouwman, M., Dronkers, E., Simões, F.C., Riley, P.R., Goumans, M.-J., Smits, A.M., and Bakkers, J. (2021). Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration. Development 148, dev198937.

  22. Hegemann, N., Primessnig, U., Bode, D., Wakula, P., Beindorff, N., Klopfleisch, R., Michalick, L., Grune, J., Hohendanner, F., Messroghli, D., et al. (2021). Right‐ventricular dysfunction in HFpEF is linked to altered cardiomyocyte Ca 2+ homeostasis and myofilament sensitivity. ESC Heart Failure 8, 3130–3144.

  23. Robert Peter Wiegmann (2021). Dominant Negative Gαs mutant to block detrimental β-AR induced pathological hypertrophy in the heart. Universität Hamburg.

  24. Osorio-Conles, Ó., Vega-Beyhart, A., Ibarzabal, A., Balibrea, J.M., Graupera, I., Rimola, J., Vidal, J., and de Hollanda, A. de (2021). A Distinctive NAFLD Signature in Adipose Tissue from Women with Severe Obesity. IJMS 22, 10541.

  25. Kobayashi, H., Gieniec, K.A., Ng, J.Q., Goyne, J., Lannagan, T.R.M., Thomas, E.M., Radford, G., Wang, T., Suzuki, N., Ichinose, M., et al. (2021). Portal Vein Injection of Colorectal Cancer Organoids to Study the Liver Metastasis Stroma. JoVE 62630.

  26. Dill, T.L., Carroll, A., Pinheiro, A., Gao, J., and Naya, F.J. (2021). The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition. Development 148, dev194027.

  27. Thesis: Helena Fisk (2020) Adipose tissue inflammation in obesity and the influence of marine long chain polyunsaturated omega-3 fatty acids, University of Southampton, of Medicine, PhD Thesis.

  28. Krystyna Anna Gieniec (2020). Investigating the Contribution of Specific Cancer-Associated Fibroblast Subsets to Colorectal Tumourigenesis

  29. de Bakker, D.E.M., Dronkers, E., Bouwman, M., Vink, A., Goumans, M.-J., Smits, A.M., and Bakkers, J. (2020). Prrx1b directs pro-regenerative fibroblasts during zebrafish heart regeneration. bioRxiv.

  30. Fischer, A., Bockstahler, M., Müller, A.-M., Stroikova, V., Leib, C., Pfitzer, G., Katus, H.A., and Kaya, Z. (2019). FN14 Signaling Plays a Pathogenic Role in a Mouse Model of Experimental Autoimmune Myocarditis. Journal of Cardiac Failure 25, 674–685.

  31. Rabacal, W., Schweitzer, F., Rayens, E., Tarantelli, R., Whang, P., Jimenez, V.C., Outwater, J.A., and Norris, K.A. (2019). Statin treatment prevents the development of pulmonary arterial hypertension in a nonhuman primate model of HIV-associated PAH. Sci Rep 9, 19832.

  32. Arunsan, P., Ittiprasert, W., Smout, M.J., Cochran, C.J., Mann, V.H., Chaiyadet, S., Karinshak, S.E., Sripa, B., Young, N.D., Sotillo, J., et al. (2019). Programmed knockout mutation of liver fluke granulin attenuates virulence of infection-induced hepatobiliary morbidity. ELife 8.

  33. Romano, G., Reggi, S., Kutryb-Zajac, B., Facoetti, A., Chisci, E., Pettinato, M., Giuffrè, M.R., Vecchio, F., Leoni, S., De Giorgi, M., et al. (2018). APOA-1Milano muteins, orally delivered via genetically modified rice, show anti-atherogenic and anti-inflammatory properties in vitro and in Apoe atherosclerotic mice. International Journal of Cardiology 271, 233–239.

  34. Rinrada Kietadisorn (2018). Drainage versus defense: The management of vascular leakage in cardiovascular diseases, Maastricht University.

  35. Hollenbach, M., Thonig, A., Pohl, S., Ripoll, C., Michel, M., and Zipprich, A. (2017). Expression of glyoxalase-I is reduced in cirrhotic livers: A possible mechanism in the development of cirrhosis. PLOS ONE 12, e0171260.

  36. MARCIO APARECIDO PEREIRA (2016). Tratamento com células derivadas do fígado embrionário retarda a progressão da fibrose hepática em ratos. Universidade de São Paulo.

Links

  1. Mondor Biomedical Research Institute

  2. Fibrosis (bio-protocol exchange)

Other (third party) tools for the same problem

  1. Medindo fibrose com ImageJ/Measuring fibrosis with ImageJ (Portuguese)
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