Bioformats Importer Importing Image Stacks of Diminished Intensity


I am having an issue when I open my time-lapse images on Fiji through bioformats importer. The first image stack opens up fine and looks pretty much how it looked when I took the image on our scope. Every single spot beyond that opens and visually looks about 2/3 dimmer. I am not sure if this is just a visual bug and the pixel intensity values are actually more representative of what I see on our scope or if the images are actually different somehow (which would be a huge problem as I am quantifying intensity of a fluorescent reporter). Have any of you heard of this issue before? I am not opening the files correctly? Any suggestions or insight would be greatly appreciated.



Hey @Tony_Desotell

Welcome to the Forum! Others on here might be able to give you more insightful help…

But to get you started on something - I’d say look at the numbers. Your instinct is correct - this might just be a rendering issue. So try adjusting Brightness & Contrast to see if it is a simple visual issue and of course, look at your Histogram - the pixel values are what matters in the end - right?!

eta :slight_smile:

The pixel values are actually being changed. I compared the intensity for a given spot after exporting a single spot vs. that same spot exported through bioformats and the intensity is roughly double.


Honestly, I am not sure what to tell you. What file format are you using here? You can always post a bug report on the Bio-Formats page.

On that page - they say before you report … “If you think you have found a bug in Bio-Formats, the first thing to do is update your version of Bio-Formats to the latest version to check if the problem has already been addressed. The Fiji updater will automatically do this for you, while in ImageJ you can select Plugins ‣ Bio-Formats ‣ Update Bio-Formats Plugins.” The newest version - 5.5.2 - was just released (see this forum post). There is also a list of “Common Issues” - just read the whole page and you’ll see how best to proceed.

Sorry - that’s all I can do to help in this at the moment…