The methods project required students to create a multi-panel scientific figure of an interspecific interaction. A methods section was then created by the student to describe in detail how to replicate the figure created. The purpose of the project was to be able to see if the methods that were written could lead to an accurate replication of the multi-panel figure created. There were three separate panels in the figure that consisted of lichen and a tree. The differences observed in this figure was of background, color, and labeling. These differences were a result from the differences in weather and positioning of the photo.
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Suggestion
In this paragraph, you write in very general terms about the methods project. I am assuming you are using this as part of your introduction to your manuscript. If so I would use a more active voice in describing what YOU did, not what students generally did. Instead of "a methods section was then created by the student" you could say "I created a methods section..."
Grammar
"The differences observed in this figure was of background, color, and labeling."
Because your subject is plural, you should use "were" instead of "was", like you did in the following sentence.