Warp Tomogram generation
185 views
Skip to first unread message
Doulin Shepherd
May 7, 2024, 11:00:13 PM5/7/24
to Warp
Hello Everyone,
Warp version: 1.1.0 (also tried 1.0.9)
Inputs: Non-gain-normalized LZW TIFF files from a K3 and Tomography 5
I am currently facing some issues with the contrast of the tilt series (.st) files generated by Warp. This is strange because the contrast of the individual tilt images looks good in the real space window. I have attached an image to clarify what I mean by contrast issue.
Initially, I thought it was a gain file problem, as Tomography 5 provides a gain file (TIFF) for each tilt series. Therefore, I acquired the super-resolution dm4 gain file and converted it to MRC using IMOD (dm2mrc), then I binned it by 2 since I didn't collect my data in super-resolution. However, the issue persisted. I also tried flipping the gain in the Y-direction and not flipping the gain, but the result was still the same.
I used both the TIFF gain from Tomography 5 and the MRC gain file I created as inputs in MotionCor2/3, and the output tiltseries look fine.
I would be grateful if someone could tell me where I am going wrong.
Warp version: 1.1.0 (also tried 1.0.9)
Inputs: Non-gain-normalized LZW TIFF files from a K3 and Tomography 5
I am currently facing some issues with the contrast of the tilt series (.st) files generated by Warp. This is strange because the contrast of the individual tilt images looks good in the real space window. I have attached an image to clarify what I mean by contrast issue.
Initially, I thought it was a gain file problem, as Tomography 5 provides a gain file (TIFF) for each tilt series. Therefore, I acquired the super-resolution dm4 gain file and converted it to MRC using IMOD (dm2mrc), then I binned it by 2 since I didn't collect my data in super-resolution. However, the issue persisted. I also tried flipping the gain in the Y-direction and not flipping the gain, but the result was still the same.
I used both the TIFF gain from Tomography 5 and the MRC gain file I created as inputs in MotionCor2/3, and the output tiltseries look fine.
I would be grateful if someone could tell me where I am going wrong.
Alister Burt
May 10, 2024, 4:30:36 PM5/10/24
to Doulin Shepherd, Warp
Hi Doulin,
Thanks for the report! I’m not immediately sure what’s going on here. The 1.1.0 code is now quite out of date and we’ll be releasing a new version soon - could you send me a link to download this gain/tilt series so I can check that everything works as expected with the latest code? 🙂
Cheers,
Alister
Sent from mobile - apologies for brevity
On May 8, 2024, at 04:00, Doulin Shepherd <doulin....@gmail.com> wrote:
Hello Everyone,
--
You received this message because you are subscribed to the Google Groups "Warp" group.
To unsubscribe from this group and stop receiving emails from it, send an email to warp-em+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/e278a932-f816-46cd-baf0-b3c94e8727f2n%40googlegroups.com.
<warp problem.PNG>
Doulin Shepherd
May 10, 2024, 4:30:55 PM5/10/24
to Alister Burt, Warp
Hi Alister,
I've sent you a link containing a subset of my data for your review. Included are the frames, the gain from the K3, the gain that Tomography 5 provides, and the defect map files.
Cheers,
Doulin
I've sent you a link containing a subset of my data for your review. Included are the frames, the gain from the K3, the gain that Tomography 5 provides, and the defect map files.
Cheers,
Doulin
Reply all
Reply to author
Forward
0 new messages