The Methods Section

This is the "how" section of your research report. Precision and exact details are key to this section, but do not include irrelevant material. This concrete infomation is usually presented in simple past tense, either active voice (We collected water samples every three days) or passive voice (Samples were collected every three days).   The ultimate test of a well-written Methods section is in replicability -- could someone else reproduce the study given what you wrote?

Include enough information about materials and methods to enable another suitably qualified person to repeat your experiments. Relegate tedious but necessary details to an Appendix, so that there are no breaks in the flow of ideas in your presentation. from "How to Write a Thesis"

The methods section generally includes three types of information: 

Most commonly, some mention of "participants/subjects/substance" (whatever passes for that which was experimented upon) is discussed first, though this is not always the case.  For example, if you performed the same procedure on three different groups, you may choose to explain the procedure in detail first, then lay out the composition of the groups.  Or, if you have three different procedures on the same type of group, you'd more logically start with the "group" and proceed to procedure.  Also, if your work involves multiple tests, then the Methods may be organized topically according to test with parallel organization shared among all.

As always, if you have a complicated Methods that you are not sure how to lay out, look for a research article that deals with a similar issue and model your organization after theirs!

Also, check with your PI/mentor/supervisor/ lab leader regarding using the traditional citation system as a means of writing your Methods section.  For many, the method was actually performed by other researchers (or your PI!), and you are applying that Method to a different set of subjects.  In this case, you may get to use the publishable shortcut and cite the part of the procedure with "...was performed as in X, Y, Z (2004)."  On the other hand, your PI may want you to experience the full glory of writing every step out in excruciating detail.

Keep in mind that whatever is in Methods should find a corresponding mention in Results.   You may want to organize the Methods section so that you can use the parallel organization (or pretty similar) in the Results section.

Example (from Rothschild, G., Nelken, I., & Mizrahi, A. (2010). Functional organization and population dynamics in the mouse primary auditory cortex. Nature Neuroscience, 13, 353-360, DOI:10.1038/nn.2484):

           Animal preparation.

We used male and female NMRI mice* (total of n = 28 mice, 8–12-weeks-old), anesthetized using ketamine (100 mg per kg of body weight) and medetomidine (0.83 mg per kg). Depth of anesthesia was assessed by monitoring the pinch withdrawal reflex. Dextrose-saline was injected subcutaneously to prevent dehydration. Body temperature was maintained at 36–38 C. The skull was exposed, cleaned and dried. A metal pin was glued to the skull and attached to a custom-made head holder allowing precise orientation of the head relative to the objective. The muscle overlying the left auditory cortex was removed and a craniotomy (~3 3 mm) was performed. The dura was gently removed and the cortical surface was kept continuously moist. Following each experiment, animals were killed by overdose with sodium pentobarbital. All experiments were approved by the Hebrew University Animal Care and Use Committee.

           Dye loading and two-photon imaging.

The auditory cortex was loaded with Fluo-4 a.m. (F14201, Invitrogen) using multicell bolus loading14. Fluo-4 a.m. was dissolved in 20% Pluronic F-127 in DMSO (vol/vol, P-6867, Invitrogen) to a concentration of 10 mM and further diluted tenfold in external buffer containing 125 mM NaCl, 5 mM KCl, 10 mM glucose, 10 mM HEPES, 2 mM CaCl2, 2 mM MgSO4 and 0.1 mM sulforhodamine 101

* NPG claims that "Nature journals like authors to write in the active voice ('we performed the experiment...') as experience has shown that readers find concepts and results to be conveyed more clearly if written directly." ( -- and yet you will see that the rest of this Nature publication is written in the passive voice. This is not an evil writing choice! Passive voice is used when the object of an action is the topic of the discourse; that is, when what is being done (or done unto) is what the paragraph is about.  So, after making it clear that human scientists were the ones performing the activities by using the active voice to get the section started, the rest of the paragraph can focus on what was done. Try turning every sentence into the active voice and see how very strange it sounds! The constant "we...we...we..." becomes mighty intrusive.

For an example, see this image: 



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