MICC Cell Observatory Made in Weizmann

WIS-NeuroMath - is a software tool for automated analysis and quantification of fluorescent microscopy images of Nerve cells, in both in vivo and in vitro preparations. This tool detects candidate neurites using a state-of-the-art edge detection algorithm proposed by Galun, Basri and Brandt at the department of computer science and applied mathematics. The method allows accurate detection of neurites in challenging images. WIS-NeuroMath was developed by Ofra Golani and Meirav Galun in collaboration with Prof. Michael Fainzilber and Dr. Ida Rishal from the department of biological Chemistry. Recently we are using it also to quantify angiogenesis.

WIS-NeuroMath is based on accurate detection of candidate neurites using the algorithm described by Galun et al (2007). It first looks for edges in the image and then matches pairs of nearly parallel edges to find fibers, which constitute neurite-like structures. The method allows accurate detection of neurites in challenging images. Following neurite detection, different types of processing can be carried out depending on the desired application:

Cell Morphology of cultured neurons

Cell bodies are detected using the same image used for neurite detection. Candidate neurites are then traced to allow assignment to the relevant cell bodies. Neurite lengths, branching, cell body area and other parameters are then calculated and saved for each cell, while ignoring irrelevant items (neurites which are not attached to cell bodies, cell bodies that are too small or too big, etc.). Individual cell data are exported to Excel files, as well as image averages. The graphical user interface allows the user to modify detection thresholds and analysis parameters, to perform analyses on single files or whole directories, and to browse through the results.

Neurite Length Analysis on Sections

This mode provides a solution for images in which cell bodies are not present, for example longitudinal nerve sections that contain only neurites and non-neuronal cells. Neurites are detected and connected component analysis is applied to distinguish between neurite elements. A user-set threshold allows exclusion of very short neurite elements if desired, to reduce noise in certain experiments. The number of neurite elements, their average and median length are calculated as well as additional parameters such as the number of branches and the branching complexity.

Ganglion Explant Analysis

Ganglion explant cultures represent a particular challenge since neurites can be very profuse and dense close to the ganglion, and even a human eye cannot distinguish between them. Hence, in this mode the user manually defines an ellipse mask around the ganglion. The software then detects neurites and counts the number of neurites crossing that mask. Neurite numbers can be calculated at several offsets inside and outside the mask, to provide average and median numbers of crossing neurites. The user can set numbers of offset masks and the distance between them as desired.

Download

Please note that this download page is intended for research purposes only.

When you download the software you agree to the terms in the Software licence.

Download Software (zip file). The zip file includes WIS-NeuroMath executable together with few images that will enable you to test it. See documentation for installation instruction.

Download Documentation (PDF).

WIS-NeuroMath is a compiled Matlab application. To use it, you should download and install the proper version of Matlab Runtime Component (MCR)
on your computer: MCRInstaller for Win 32bit or MCRInstaller for Win 64bit.

News

Oct 10, 2011:
Version 3.4.8 is now available and supports many new features.
If you have any question please contact us.

Please credit WIS-NeuroMath by citing the following two papers

Citations:

1. M. Galun, R. Basri and A. Brandt, "Multiscale edge detection and fiber enhancement using differences of oriented means", ICCV, 2007
2. I. Rishal, O. Golani, M. Rajman, B. Costa, K. Ben-Yaakov, Z. Schoenmann, A. Yaron, R. Basri, M. Fainzilber and M. Galun, “WIS-NeuroMath enables versatile high throughput analyses of neuronal processes” Developmental Neurobiology, 2012.

We will appreciate if you would update us with any publication using the tool.

Publications Using Results Obtained With WIS-NeuroMath

1. Naftelberg S., Abramovich Z., Gluska S, Yannai S, Joshi Y., Donyo M., Ben-Yaakov K., Gradus T., Zonszain J., Farhy C., Ashery-Padan R., Perlson E., Ast G. (2016), "Phosphatidylserine Ameliorates Neurodegenerative Symptoms and Enhances Axonal Transport in a Mouse Model of Familial Dysautonomia". PLOS Genetics. doi: 10.1371/jurnal.pgen.1006486
2. Zuko A., Ouro-And A., Post H., Taggenbrock R.L.R.E., vanDijk R.E., Altelaar A.F.M., Heck A.J.R., Petrenko A.G., van der Zwaag B., Shimoda Y., Pasterkamp R.J., Burbach J.P.H.. (2016).  "Association of Cell Adhesion Molecules Contactin-6 and Latrophilin-1 Regulates Neuronal Apoptosis". Frontiers in Molecular Neuroscience. doi 10.3389/fnmol.2016.00143
3. Danelon V., Montroull L.E., Unsain N., Barker P.A., Masco D.H. (2016). "Calpain-dependent truncated form of TrkB-FL increases in neurodegenerative processes". Molecular and cellular Neuroscience. doi: 10.1016/j.mcn.2016.07.002
4. Ben-Tov Perry R., Rishal, I., Doron-Mandel E., Kalinski A.L., Medzinhradsky K.F., Terenzio M. Alber S., Koley S., Lin A., Rozenbaum M., Yudin D., Sahoo P.K., Gomes C., Shinder V., Geraisy W., Huebner E.A., Woolf C.J., Yaron A., Burlingame A. L., Twiss J.L., Fainzilber M. (2016). "Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size". Cell Reports. doi: 10.1016/j.celrep.2016.07.005
5. Eckharter C., Junker N., Winter L., Fischer I., Fogli B., Kistner S., Pfaller K., Zheng B., Wiche G., Klimaschewski L., Schweigreiter R. (2015), "Schwann cell expressed  Nogo-B modulates axonal branching of adult sensory neurons through the Nogo-B receptor NgBR". Frontiers in Cellular Neuroscience. doi: 10.3389/fncel.2015.00454
6. Fannon, J., Tarmier, W. and Fulton, D. (2015), "Neuronal activity and AMPA-type glutamate receptor activation regulates the morphological development of oligodendrocyte precursor cells". Glia. doi: 10.1002/glia.22799
7. Oguro-Ando A., Rosensweig C., Herman E., Nishimura Y., Werling D., Bill R., Berg J.M. Gao F., Coppola G., Abrahams B.S., Geschwind D.H. (2015), "Increased CYFIP1 dosage alters cellular and dendritic morphology and dysregulates mTOR". Molecular Pyschiatry. doi: 10.1038/mp.2014.124
8. Marvaldi, L., Thongrong, S., Kozłowska, A., Irschick, R., Pritz, C. O., Bäumer, B., Ronchi, G., Geuna, S., Hausott, B. and Klimaschewski, L. (2014), "Enhanced axon outgrowth and improved long‐distance axon regeneration in sprouty2 deficient mice". Devel Neurobio. doi:10.1002/dneu.22224
9. Painter M.W., Brosius-Lutz A., Cheng Y-C., Latremoliere A., Duong K., Miller C.M., Posada S., Cobos E.J, Zhang A.X., Wagers A.J., Havton L.A., Barres B., Omura T., Woolf C.J. (2014). "Diminished Schwann Cell repair Responses Underlie Age-Associated Impaired Axonal Regeneration". Neuron. doi: 10.1016/j.neuron.2014.06.016
10. Rishal I., Kam N., Ben-Tov Perry R., Shinder V., Fisher E M.C. , Schiavo G. & Fainzilber M., 2012: "A Motor-Driven Mechanism for Cell-Length Sensing". Cell Reports, Volume 1, Issue 6, 608-616.
11. Ben-Yaakov K., Dagan SY, Segal-Ruder Y, Shalem O, Vuppalanchi D, Willis DE, Yudin D, Rishal I, Rother F, Bader M, Blesch A, Pilpel Y, Twiss JL & Fainzilber M., 2012: "Axonal transcription factors signal retrogradely in lesioned peripheral nerve". EMBO Journal 31, 1350 – 1363.
12. C.H. Ma, G.J. Brenner, T. Omura, O.A. Samad, M. Costigan, P. Inquimbert, V. Niederkofler, R. Salie, H.Y. Lin, S. Arber, G. Coppola, C.J. Woolf, and T.A. Samad. (2011) The BMP co-receptor RGMb promotes while the endogenous BMP antagonist Noggin reduces neurite outgrowth and peripheral nerve regeneration by modulating BMP signaling. Journal of Neuroscience 31: 18391-18400.