Noisy corrected Image

[Aliya1214]

Hey,

I have an image stack of a rat brain acquired with light sheet fluorescence microscopy, focusing on the tumor channel. The tumor cells are GFP-transfected and imaged in the green channel, but the data is quite noisy due to autofluorescence. In addition, there’s a noticeable intensity difference across tiles from stitching (Fig A).

I tried using BaSiC in Fiji on the NIFTI stack, but instead of correcting the autofluorescence and stitching artifacts, the output looked very different from what I expected (Fig B).

Do you have any suggestions on how to better remove the autofluorescence or handle the stitching issues?

Thanks,
Aliya