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SchmollerLab / Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
BSD 3-Clause "New" or "Revised" License
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0 values were rendered by ACDC when measuring fluorescent signals. #534

Open CorneliusWang753 opened 1 month ago

CorneliusWang753 commented 1 month ago

Description:

We used mito-roGFP to measure the redox state of yeast cells expressing this biosensor. We calculated the ratio b/w reduced and oxidized mito-roGFP signals using the Nikon software NIS-Element. An image wherein the ratio was illustrated as a signal was produced and then exported using the same software. The Bright Field view of the original image and the generated ratio view were combined using Fiji ("merge channel"). This combined file was fed to ACDC for analysis: the purpose of this was to quantify the ratio of several individual cells across a given time period. However, even though the signals looked clear on both NIS-Elements and Fiji, ACDC produced many "0" values under the "ratio" measurement. In the example we attached, please look under cell ID 4 and take note of the many "0" value under "Ratio_Mean". We are not sure if this is caused by some setting issue in ACDC, or by the fluorescent images themselves. The images were obtained via a microfluidic chamber plus long-term imaging. Please let us know if you believe this is caused by using ACDC incorrectly or by something with the images.

AllPos_acdc_output.xlsx

ElpadoCan commented 1 month ago

Hi @CorneliusWang753, I'm sorry to hear you are experiencing issues but rest assured we'll fix them.

However, I have a couple of questions. Is the merged channel manually added to the Images folder? Is the Ratio_mean defined as a combined or custom metric?

If possible, it might be faster for me if you could share the position folder with instructions on how to replicate. You can share it with a cloud of your choice to my email padovaf@tcd.ie. Thanks!

Cheers Francesco