Stacking frames extracted from movie - which software

zzffnn · Post by **zzffnn** » Sun Feb 19, 2017 6:31 pm

I would like to convert a video into serial individual frames, for focus stacking fast moving subjects that occasionally pause for a second or two (for example, a live ciliate under microscope).

I did forum search using keywords "stacking video", read most relevant threads and found the following:

1) CombineZP (free)

2) Helicon Focus ( not sure how much?)

3) Magic Lantern (Canon only, free)

4) Photoshop CS6 ($10 per month to rent, $700 to buy?)

Edit:

5) VLC (free) seems to be able to do it serially too:
https://www.google.com/amp/m.wikihow.co ... %3Famp%3D1

Am I missing any other popular choices? What are pros and cons of each program? I am willing to pay more for convenience and quality, but CS6 is too expensive, considering I don't use it that much and it is $120/year to rent only, not own.

I have Olympus E-PM2 (micro 4/3, mirrorless) and Windows 8 currently. Will probably upgrade to Panasonic GH5 in the future.

Thank you very much!

Edit 2:

A sports software named Kinovea can do this, but extracted frames seem to be limited to 720p, whereas VLC can do 1080p.

JH · Post by JH » Mon Feb 20, 2017 1:13 pm

Probably of marginal use for non Canon users. I use Canon's EOS MOVIE Utility to exract photos from videos (.MOV format). Then I stack them in Zerene.
Regards Jörgen

soldevilla · Post by **soldevilla** » Mon Feb 20, 2017 2:44 pm

PIPP alow to convert the frames of an AVI video to pictures.

Grahame · Post by **Grahame** » Wed Feb 22, 2017 6:55 pm

I've used VLC for another purpose where I wanted to capture every 5th etc frame.
It will capture all frames.
Worked perfectly.
It's a great video player to have around, not much it won't play.
Of course being free is another added bonus.
I doubt you will be disappointed.

JL · Post by JL » Fri Feb 24, 2017 8:56 am

I have used Helicon Focus for that particular purpose, by loading 4K snippets shoot with Panasonic cameras, it does work well. I guess that you can download the program and try it.

jnh · Post by **jnh** » Fri Feb 24, 2017 11:43 am

I'd recommend ImageJ (or its cousin FIJI) for that purpose. It's free/open source and very useful for a number of arcane tasks.

zzffnn · Post by **zzffnn** » Fri Feb 24, 2017 2:25 pm

Thank you very much, everyone!

So I compared CombineZP and FIJI today. On an old Windows 8. FIJI is not very easy to use for me.

There must be things that I did wrong, as neither FIJI nor CombineZP produced good stacked images. If I have to pick one, I will pick the CombineZP stack and copy it over to a clean single frame background.

My original movie was recorded with oblique illumination and there was subject/background movement.

Most likely I did not use FIJI correctly.

I picked a movie fragment that has clear focus from subject top to bottom. Exacted 100 movie frames using CombineZP. But I could not figure out how to exact movie to frames in FIJI.

Then for CombineZP, I did "thoroughly align all frames", selected all frame to clipboard, then do all types of stacks. Pyramid weighted stack came out best to my eyes.

With FIJI, I "import"ed exacted movie frames as "image sequence", after loading completion, then I clicked on "image" - "stacks" - "Z project" and run it. "Medium intensity" method came out best. "Images to stack" did not work for me.

This is FIJI "Maximum intensity" instead of "Medium intensity".

VLC could not fully exact movie frames, on my computer. I had to exact 1 frame out of 20, otherwise VLC won't run. Ratio of 1 out 5 could not run, while ration of 1 out of 50 ran smoothly. What VLC did was really simple screen capture. I got a good frames out of my movie, instead of 100 frames exacted by CombineZP.

zzffnn · Post by **zzffnn** » Fri Feb 24, 2017 2:38 pm

jnh wrote:I'd recommend ImageJ (or its cousin FIJI) for that purpose. It's free/open source and very useful for a number of arcane tasks.

Please kindly advise me how to run FIJI in my case. A step by step dummy-proof procedure would really help me.

I figured out how to use CombineZP without reading any instruction (though I might not did it correctly). But I could not figure out FIJI.

zzffnn · Post by **zzffnn** » Fri Feb 24, 2017 3:02 pm

Helicon Focus made stacking easy (I did not read/watch any instruction):

pyramid

Depth_map (default) Radius 8 Smoothing 4

Weighted_avarage (default) Radius 8 Smoothing 4

I suspect the basic package of Zerene would be equally easy to use, and cost less than Helicon Focus? CombineZP can be used to exact movie frames just fine - Helicon results came from CombineZP exacted frames. Edit: I also did a Helicom stack using frames extracted by Helicon, from the movie. Image quality is the about the same, compared to that made from CombineZP extracted movie frames.

zzffnn · Post by **zzffnn** » Fri Feb 24, 2017 3:41 pm

Zerene is equally easy to use and stacking image quality is comparable to Helicon. Also no instruction needed for basic stacking. And much cheaper than Helicon.

jnh · Post by **jnh** » Sat Feb 25, 2017 12:07 pm

Please kindly advise me how to run FIJI in my case. A step by step dummy-proof procedure would really help me.

Yes, FIJI can be a bit confusing at first. To make single frames from your AVI file use "File > Import > AVI..." A dialog should pop up, which I think you can safely ignore and just confirm with ok. Then simply go to "File > Save As... > Image Sequence". Another dialog pops up asking about the output format for the images (TIFF, JPG etc.) and how the sequence should be numbered. After specifying a destinatuion folder in the next dialog, you should end up with individual images from your movie.

But FIJI might have trouble with some compressed (vs. uncompressed) AVI formats, maybe this is an issue you run into? Also, from your previous posts, I 'm not clear, if you also tried to do focus stacking in FIJI. While that is possible in FIJI, stacking in e.g. Zerene gives vastly better results.

zzffnn · Post by **zzffnn** » Sat Feb 25, 2017 12:20 pm

Indeed, Zerene or Helicon Focus seemed to provide much better stacking results. Even CombineZP did better with my subject.

So yes, I did try stacking with FIJI. And the images above under FIJI was stacked by FIJI. Unless I did it wrong.

Would you please let me know how to stack in FIJI? Use "Image" - "stacks"- "Z project"?

jnh · Post by **jnh** » Sat Feb 25, 2017 6:47 pm

If you use a z-projection, you'll get a maximum intensity projection, which is a quick and convenient way to collapse a confocal z-stack, but is not suitable for focus stacking.

To do focus stacking in FIJI, you need the Extended Depth of Field plugin (which I believe is not included in FIJI). Check here: http://bigwww.epfl.ch/demo/edf/

zzffnn · Post by **zzffnn** » Sat Feb 25, 2017 8:22 pm

jnh wrote:If you use a z-projection, you'll get a maximum intensity projection, which is a quick and convenient way to collapse a confocal z-stack, but is not suitable for focus stacking.

To do focus stacking in FIJI, you need the Extended Depth of Field plugin (which I believe is not included in FIJI). Check here: http://bigwww.epfl.ch/demo/edf/

Thank you very much!

How do you "open an image stack" in FIJI? "Import" - "image sequence"? I put edf plug-ins into FIJI. Then click and run the easy mode of EDf in fast mode, it is still taking a very long time...........

jnh · Post by **jnh** » Sun Feb 26, 2017 6:30 pm

Yes, you do "Import > Image Sequence". At this point you have an image sequence, which you can process with the EDF plugin.
This is nitpicky, but maybe worth pointing out: a stack has a bit of a different meaning in ImageJ/FIJI and opens up a few more tools to manipulate said stacks. You can convert a sequence to a stack with "Images > Stacks > Images to Stack" (but as mentioned above, this is not necessary for processing with the EDF plugin).