(This is based in large part on a page from the Nikon Imaging Centre at Harvard Medical School, https://nic.med.harvard.edu/equipment/materialsandmethods)
Here’s what to include in a MATERIALS AND METHODS section for the microscopy section. For a reader to assess whether you have performed experiments correctly, there are a few parameters that you need to include in your paper. This information is necessary for the reader to estimate the resolution and sensitivity of your microscope, and therefore to decide whether your data support your conclusions.
- Make and model of microscope (and imaging mode, e.g. confocal, widefield, et cetera)
- Type, magnification, and numerical aperture of the objective lenses (e.g. PlanApo chromat 63X/1.45 NA)
- Imaging enviromental conditions: chamber, media, temperature, buffer, etc.
- Filter sets (with peak transmission and bandwidth, or the manufacturer part number so the reader can look up spectra) and/or laser used
- Camera make and model
- Other motorized components used
- Acquisition software
- Any subsequent software used for image processing, with details about types of operations involved (e.g., type of deconvolution, 3D reconstructions, surface or volume rendering, gamma adjustments, etc.)
Here is an example of a Materials and Methods:
Confocal and Epifluorescence Microscopy—Immunofluorescent preparations were analyzed on the EMBL Compact Confocal Micro- scope (21) or a Zeiss Axiophot light microscope. Excitation wavelengths of 476 nm (for fluorescein isothiocyanate-coupled antibodies) or 594 nm (Texas Red-coupled antibodies) were selected. Some images presented in Figs. 5 and 8A were recorded on a Zeiss Axiovert S100 2TV DeltaVision Restoration microscope (Applied Precision) using either a Zeiss Plan-apochromat (100X, 1.40 numerical aperture objective) or a Zeiss Plan-neofluar (40X, 1.30 numerical aperture objective) and a CCD-1300-Y/HS camera (Roper Scientific), using the standard 4-colour filterset present on the deltavision. Images were captured and processed by constrained iterative deconvolution using SoftWorx (Applied Precision) and prepared as illustrations using Adobe Photoshop. Two-dimensional images presented here are maximal intensity projections of three-dimensional volumes along the optical axis.