This page provides links to variety of useful microscopy related tools, documents and other resources.

FIJI (also known as Image J) is an open-source image processing package which bundles a lot of plugins to facilitate scientific image analysis.

Desktop software to work on images collected on Zeiss instruments (.czi files)

    • [ddownload id="1316" style="link" text="Basics of Image Processing with ZEN Lite"]

A useful tutorial and information for using ZEN software and optimising image display and processing.

Desktop software to work on images collected on Leica instruments (.lif files)

An open-source, community-edited database of fluorescent proteins and their properties.  To cite FPbase use: Lambert, TJ (2019) FPbase: a community-editable fluorescent protein database. Nature Methods. 16, 277–278. doi: 10.1038/s41592-019-0352-8

A list of fluorescent dyes, their properties and associated Zeiss filter sets.

A useful, customisable tool for combining and visualising fluorophore and filter properties.

Unpublished methods, information & protocols

  • Sectioning
    • Hand sectioning fresh plant tissues – Download
    • Vibratome sectioning guide – Download
  • Staining
    • Routine staining protocols for fresh and fixed plant tissue – Download
    • Vital staining in plant tissues information and protocols – Download
    • Simple fungal staining in plant tissues – Download
  • Embedding
    • LRW resin embedding protocol – Download
    • LRW resin embedding for GUS stained tissue protocol – Download
    • Molecular microscopy and nucleic acid localisation information and overview – Download


Published methods

  • Rae A.E., Rolland, V., White R.G., Mathesius U. (2021). New methods for confocal imaging of infection threads in crop and model legumes. Plant Methods 17, 24.
  • Rolland V (2018). Determining the Subcellular Localization of Fluorescently Tagged Proteins Using Protoplasts Extracted from Transiently Transformed Nicotiana benthamiana Leaves. In: Covshoff S. (eds) Photosynthesis. Methods in Molecular Biology, vol 1770. Humana Press, New York, NY.
  • Ayliffe M, Periyannan S, Feechan A, Dry I, Schumann U, Lagudah E, Pryor A (2014). Simple Quantification of In Planta Fungal Biomass. In: Birch P., Jones J., Bos J. (eds) Plant-Pathogen Interactions. Methods in Molecular Biology, vol 1127. Humana Press, Totowa, NJ.
  • Talbot M.J., White R.G. (2013). Methanol fixation of plant tissue for Scanning Electron Microscopy improves preservation of tissue morphology and dimensions. Plant Methods 9, 36.
  • Talbot M.J., White R.G. (2013). Cell surface and cell outline imaging in plant tissues using the backscattered electron detector in a variable pressure scanning electron microscope. Plant Methods 9, 40.


  • Stoddard A & Rolland V (2019). I see the light! Fluorescent proteins suitable for cell wall/apoplast targeting in Nicotiana benthamiana leaves. Plant Direct. 2019; 3: 115.
  • Reynolds KB, Cullerne DP, El Tahchy A, Rolland V, Blanchard CL, Wood CC, Singh SP, Petrie JR (2019). Identification of Genes Involved in Lipid Biosynthesis through de novo Transcriptome Assembly from Cocos nucifera Developing Endosperm, Plant and Cell Physiology, Volume 60, Issue 5, 2019, 945–960.
  • Vanhercke T, Belide S, Taylor MC, El Tahchy A, Okada S, Rolland V, Liu Q, Mitchell M, Shrestha P, Venables I, Ma L, Blundell C, Mathew A, Ziolkowski L, Niesner N, Hussain D, Dong B, Liu G, Godwin ID, Lee J, Rug M, Zhou X‐R, Singh SP and Petrie JR (2019). Up‐regulation of lipid biosynthesis increases the oil content in leaves of Sorghum bicolor . Plant Biotechnol J, 17: 220-232.
  • Rolland V, Rae BD, Long BM (2017). Setting sub-organellar sights: accurate targeting of multi-transmembrane-domain proteins to specific chloroplast membranes, Journal of Experimental Botany, Volume 68, Issue 18, 2, 2017, 5013–5016.
  • Allen RS, Tilbrook K, Warden AC, Campbell PC, Rolland V, Singh SP and Wood CC (2017). Expression of16 Nitrogenase Proteins within the Plant Mitochondrial Matrix. Front. Plant Sci. 8:287.
    https://doi: 10.3389/fpls.2017.00287
  • Zhi Y, Taylor MC, Campbell PM, Warden AC, Shrestha P, El Tahchy A, Rolland V, Vanhercke T, Petrie JR, White RG, Chen W, Singh SP and Liu Q (2017). Comparative Lipidomics and Proteomics of Lipid Droplets in the Mesocarp and Seed Tissues of Chinese Tallow (Triadica sebifera). Front. Plant Sci. 8:1339.
    https://doi: 10.3389/fpls.2017.01339

Online resources

  • Zeiss Campus
    A wide selection of web resources, tutorials and articles covering many aspects of light microscopy
  • iBiology microscopy series
    A series of webpages with videos providing information on many aspects of light microscopy
  • MyScope
    Microscopy Australia’s online training resource


Societies and journals