open-discussion
20322 Subscribers 
open-discussion > Tools available to detect brightness(fluorescence) changes in calcium images after virus expression
Showing 1-1 of 1 posts
Dec 14, 2020 10:12 PM | Meen Ven
Tools available to detect brightness(fluorescence) changes in calcium images after virus expression
Hi
I have 3d tiff stacks from in vivo 2 photon calcium imaging from 2 different days of the same mouse brain areas (imaged along axial plane).I want to detect possible increases in fluorescence due to virus expression between the 2 days.
Images mostly contain dendritic structures only. I'd like to know what tools are available for this type of task ?
I tried Vaa3d, simple neurite trace in ImageJ. I think that these tools trace the dendritic paths along the axial plane, which is great. But i would like to know how to detect changes in fluorescence ?
Both 3d tiff stacks have slightly different brightness histograms. Imaging conditions are kept uniform across days.
Should i do the routine image preprocessing between the 2 3d tiff stacks (like normalization, background subtraction, histogram matching etc).
Kindly advise.
I have 3d tiff stacks from in vivo 2 photon calcium imaging from 2 different days of the same mouse brain areas (imaged along axial plane).I want to detect possible increases in fluorescence due to virus expression between the 2 days.
Images mostly contain dendritic structures only. I'd like to know what tools are available for this type of task ?
I tried Vaa3d, simple neurite trace in ImageJ. I think that these tools trace the dendritic paths along the axial plane, which is great. But i would like to know how to detect changes in fluorescence ?
Both 3d tiff stacks have slightly different brightness histograms. Imaging conditions are kept uniform across days.
Should i do the routine image preprocessing between the 2 3d tiff stacks (like normalization, background subtraction, histogram matching etc).
Kindly advise.