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I am working on a Field trial with small research plots. I've created a GeoTiff orthomosaic with 4 bands from a multispectral camera (Red, Green, NIR, Red Edge) and want to be able to extract the mean pixel value for each band in each plot using ArcGIS. I have tried creating a fishnet grid to cover each plot, but am having trouble getting it to align. Furthermore, once I've created my fishnet, I'm not entirely sure what to do next.

Would I use the Zonal Statistics toolbox to do this?

Also, is there a simpler way of doing this, for instance creating a simple polygon around a plot and then computing the values for each band?

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I believe one way to achieve this would be to use Zonal Statistics as Table tool.

You would need to draw multiple polygons around your plots (I assume because you said "small research plots", this wouldn't be too time consuming) as a single shapefile, and give each a unique ID. When I have done this in the past for the very same reason my plots were identified from north to south going east to west. This makes it easy to describe in text if you need it for a report.

Then using the Zonal Statistics as Table tool you just:

  1. Insert the shapefile as the "Feature zone data".
  2. Select the unique ID field as the "Zone field".
  3. Select your output directory
  4. Insert your bands as the "Input value raster" parameter (you made need to do this individually and treat them as individual geotiffs).
  5. Select your Statistic type (e.g. mean)

If you do need to treat each band as individual rasters then it would be beneficial to run the process as a batch job for the four bands.

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