cryo-EM TIFF movies to single low-res jpg

[Jerry (Fengbin) Wang]

Dear EMAN2 users and developers

I am wondering whether there is a quick method in EMAN2 to convert TIFF movies (40 frames) into low-res jpgs? As sometimes, we want to look at jpgs first to select movies, while jpgs are not always provided.

I tried a few things in e2proc2d but couldn't find a way to add 40 frames in the TIFF together (without alignment)

Many thanks

Jerry

[Ludtke, Steven J.]

Not sure exactly what "low res" means in this case, but you can certainly use 

e2proc2d.py file.tif file.jpg --average

or if you're after a "thumbnail" or somesuch

e2proc2d.py file.tif file.jpg --meanshrink 12 --average

In general:

e2proc2d.py --help

and

e2help.py processors

should give you information on most of what you need. 

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

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[Ludtke, Steven J.]

Maybe worth mentioning the less obvious wildcard mechanism (it  is mentioned in --help) too:

e2proc2d.py *.tif @.jpg --meanshrink=12 --average

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

On Feb 19, 2024, at 1:24 PM, Jerry (Fengbin) Wang <jerry...@gmail.com> wrote:

[Jerry (Fengbin) Wang]

Many thanks Steven! I didn't put --meanshrink before --average which caused the problem

I have a follow-up question. When I ran this command 

e2proc2d.py input.tif output.png --meanshrink=4 --average

The output file looks perfect if I opened it by e2display. However, in a Mac folder, the preview looks dark. The meanshrink=12 file looks more bright. Is there a fix to this?

[Ludtke, Steven J.]

The default for PNG images is 16 bit output, and the values may not span the 16 bit range without scaling. If you do:

e2proc2d.py input.tif output.png:8 --meanshrink=4 --average

it should generate 8 bit PNGs instead

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

On Feb 19, 2024, at 2:48 PM, Jerry (Fengbin) Wang <jerry...@gmail.com> wrote:

Many thanks Steven! I didn't put --meanshrink before --average which caused the problem

I have a follow-up question. When I ran this command 

e2proc2d.py input.tif output.png --meanshrink=4 --average

The output file looks perfect if I opened it by e2display. However, in a Mac folder, the preview looks dark. The meanshrink=12 file looks more bright. Is there a fix to this?

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/34ad9e3b-312a-4bba-82a9-801c0e5eb46an%40googlegroups.com.
<image.png>

[Sen, Anindito]

Thanks Guys,

I was also about to enquire about this.  

Stay safe & Regards

Anindito Sen. Ph.D

Microscopy and Imaging Center 
Texas A&M University

301 Old Main Dr

College Station, TX 77843-2257

 

Office: ILSB Room 1133
Tel. 979-458-9881
fax: 979-847-8933

http://microscopy.tamu.edu

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From: em...@googlegroups.com <em...@googlegroups.com> on behalf of Ludtke, Steven J. <slu...@bcm.edu>
Sent: Monday, February 19, 2024 2:20 PM
To: em...@googlegroups.com <em...@googlegroups.com>
Subject: Re: [EMAN2] cryo-EM TIFF movies to single low-res jpg

 

Maybe worth mentioning the less obvious wildcard mechanism (it is mentioned in --help) too: e2proc2d. py *. tif @. jpg --meanshrink=12 --average --- Steven Ludtke, Ph. D. <sludtke@ bcm. edu> Baylor College of Medicine Charles C. Bell Jr. , Professor

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[Jerry (Fengbin) Wang]

Oops, I got this after adding :8

Is it my python or Eman2 version problem?

Many thanks!

Regards,

Jerry

[Ludtke, Steven J.]

Your installed version may be too old. You can try --outmode=uint8 instead?

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

On Feb 19, 2024, at 5:59 PM, Jerry (Fengbin) Wang <jerry...@gmail.com> wrote:

Oops, I got this after adding :8

Is it my python or Eman2 version problem?

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/82c31796-716b-413b-ba73-a0043a58fef2n%40googlegroups.com.

[Jerry (Fengbin) Wang]

Many thanks Steven! I still have some issues in my eman2 version, but I figured out a two-step command to get around this from your old posts:

e2proc2d.py 20240202_1132_A000_G000_H001_D001.tiff tmp.png --meanshrink=4 --average

e2proc2d.py tmp.png tmp.jpg --fixintscaling sane

Thanks again!

Jerry