How to create a Macro/algorithm for robust dynamic range setting in FIJI

Hi, all!

My name is Sophia and I am a beginner in FIJI. The lab group I am in is trying to develop a HTP image processing workflow for bacterial communities on human tongue dorsum using combinatorial labeling and spectral imaging. Once our images are linearly unmixed using Zen online fingerprinting, we input the .czi files to FIJI and manually adjust the dynamic range to ensure the image is at its clearest.

However, manual dynamic range setting in FIJI is a clear bottleneck to our workflow. I did some research to learn about FIJI macros, but I doubt those would be helpful because dynamic range can vary hugely for one taxa of bacterial cells from person A to person B. Therefore, automating assignment to a specific dynamic range for one bacterial taxa would be pointless and ineffective.

As a result, I was wondering if I could get any pointers on where to start with this problem. Would you have any suggestions for ways to automate/script this aspect of our workflow? Should I look into a different programming language? I’d just like some direction on how to start thinking about this problem and how to strategize a reasonable approach that meshes well with the biological constraints we are dealing with.

Thank you for your time!

dynamic range of visualization doesn’t affect at all real pixel intensity values.
I think you should move to some quantitative analysis of your experiments.
manual setting of dynamical range can bias a lot the interpretation of your experiments.
it could be useful to upload some of your images here on this forum

Hi @runner020,

As @emartini says, I can’t understand why you want to adjust dynamic range in a high throughput context? Unless what you’re actually talking about is thresholding for segmentation purposes?

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