Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Correction of parameters for SIM reconstruction #26

Open
nasful opened this issue Aug 9, 2024 · 0 comments
Open

Correction of parameters for SIM reconstruction #26

nasful opened this issue Aug 9, 2024 · 0 comments

Comments

@nasful
Copy link

nasful commented Aug 9, 2024

I am trying to reconstruct SIM images taken from Lattice light-sheet microscope. It has only one directional image and is in .tif format. I am struggling to understand the following things while running the software. Can someone kindly help me to reconstruct SIM image
To create OTF

  1. How should my input PSF be? I mean, should it be a 3D PSF stack (XYZ) without phases or should it be a 3D PSF stack of (XY, Phase, Z)?
    About the image and parameters
  2. As I understand, if I have a 3D images (XYZ) (suppose 50 z planes) where each plane is imaged 5 times for different phases (means different X-galvo positions), I can arrange my images either in a single stack in XY,phase,Z (total 50*5 = 250 number of sclices as shown in the repository data) or 50 number of XY,phase stacks with similar file name pattern. Am I correct?
  3. Since I have only one angle should I mention 0 against k0angle argument?
  4. If I have a lattice line spacing of 1 micron and if I take 5 phases in between this 1 micron, what would be the correct value of ls (1 or 0.2)?
  5. If I organize my images the way I mentioned in point 1 what would be the right value of fastSI?
  6. If my illumination objective’s NA is 0.8, and the outer and inner NA of my ring are 0.7 and 0.6 respectively what would be the right value of besselNA?
    I appreciate your support.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant