This post details Noah Kreb’s ImageJ analysis to measure oyster size and counts originally posted in the notebook post here.

Protocol

Protocol written by Noah Krebs modified 20250506

1: Download Image J. Lookup how to download this application for your device(Mac, Windows, etc).

2: Open Image J. Find the downloaded oyster images and open them.

3: Once the picture is open, set the scale using the ruler in the picture. First use the straight segment tool to make a line along the ruler that is a given distance, usually the longer the better so it is more accurate. Then you can set the scale and change the units to mm. Press analyze and then set scale to the set the scale.

4: Once that is done, you are ready to start measuring oysters! What I find helpful is using the paintbrush tool to section off the picture so you can keep track of the oysters you have already measured. When you are ready to measure the length and width of an oyster, make sure to zoom in on that given oyster and find the longest edge to edge length. Oysters come in many different shapes and sizes so don't be afraid to play around with a few different measurement points and see which one is longer. To measure these segments, simply take your straight segment tool, measure the oyster from edge to edge and then hit analyze and measure. Once this is measured, you can view it in the results section with the length being the measurement farthest to the right. Then when measuring width, you want to make a perpendicular measurement at the oyster's widest section making sure the width measurement is a perpendicular to the length measurement as possible which can be checked in the results section by seeing how close to 90 degrees the difference between the angles of the two measurements are.

5: I there is any time where you cannot make a clear measurement of an oyster, just record it as N/A so it is still included in the count. If only one measurement is able to be made, still make it but input N/A for the other measurement whether it is width or length. I have attached so examples oysters that are not able to be measured accurately so you know what to look for.

6: Once you have completed measuring your oysters, copy and paste your results onto a spreadsheet and organize it by bag. I have attached a link below of an example of how to set up a sheet to record oyster measurements.

https://docs.google.com/spreadsheets/d/1vuSWMP7jEdqdNuVmK425oe_T7iKYq43tPDdfnxHcwek/edit?gid=0#gid=0