Image sequence to video conversion (high compression): software recommendations?

[Guenter Giese]

Hi all,

I want to generate movies for publication from neuronal structures
recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image
sequences are rather large up to GB), and movie size for publication is
confined to 10 MB.


Image sequence to video conversion (high compression): which software /
codec do you recommend for preservation of small structures (cells,
axons, dendrites)?

Exact color rendition is not that critical (two-channel fluorescence
images, plus labels in different colors).

Freeware is preferred, or are there big advantages of commercial solutions?

Thank you for recommendations!

Guenter

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[Saalfeld, Stephan]

I am satisfied with avconv, the current ffmpeg replacement in the
standard Ubuntu distribution.  This command line generates an H.264
compressed movie in a Quicktime mov container at 20fps and an average
bitrate of 9600kb/s from a series of tif files with zero padded numbers
of four digits length as you can save it with ImageJ:

avconv -r 20 -i %04d.tif -f mov -vcodec libx264 -b 9600k movie.mov

Best,
Stephan



On Tue, 2014-09-16 at 15:01 +0200, Guenter Giese wrote:

> Hi all,
>
> I want to generate movies for publication from neuronal structures
> recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image
> sequences are rather large up to GB), and movie size for publication is
> confined to 10 MB.
>
>
> Image sequence to video conversion (high compression): which software /
> codec do you recommend for preservation of small structures (cells,
> axons, dendrites)?
>
> Exact color rendition is not that critical (two-channel fluorescence
> images, plus labels in different colors).
>
> Freeware is preferred, or are there big advantages of commercial solutions?
>
> Thank you for recommendations!
>
> Guenter
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Guenter,

On Tue, 16 Sep 2014, Guenter Giese wrote:

> I want to generate movies for publication from neuronal structures
> recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image
> sequences are rather large up to GB), and movie size for publication is
> confined to 10 MB.

The best way is to get down and dirty and write a little program, e.g.
using JavaCV: https://github.com/bytedeco/javacv. It is really the only
option if you want as much control as possible.

I added a very simple Beanshell snippet to

        http://imagej.net/Scripting_toolbox#Writing_out_movie_files_with_JavaCV

to give you a head start.

> Image sequence to video conversion (high compression): which software /
> codec do you recommend for preservation of small structures (cells,
> axons, dendrites)?

This, in particular, is a hard problem. You will have to experiment with
the parameters quite a bit. At least you have the option to let the
computer do the optimization, now that you have a script to write out the
movie.

Ciao,
Johannes

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[Knecht, David]

You can output Qucktime directly with the saveasmovie plugin (part of Fiji now I think).  We either do that or save as Image Sequence, import into quicktime pro (pretty inexpensive and adds lots of features to Qucktime player 7- don’t use the later player versions as they don’t work) and then export a movie.  The advantage of the quicktime pro route is the added codecs that give higher quality compression  (H264) than what saveasmovie has access to.  Dave

On Sep 16, 2014, at 9:01 AM, Guenter Giese <[hidden email]> wrote:

> Hi all,
>
> I want to generate movies for publication from neuronal structures recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image sequences are rather large up to GB), and movie size for publication is confined to 10 MB.
>
>
> Image sequence to video conversion (high compression): which software / codec do you recommend for preservation of small structures (cells, axons, dendrites)?
>
> Exact color rendition is not that critical (two-channel fluorescence images, plus labels in different colors).
>
> Freeware is preferred, or are there big advantages of commercial solutions?
>
> Thank you for recommendations!
>
> Guenter
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
Storrs, CT 06269
860-486-2200

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[Kurt Thorn]

I have had pretty good luck saving uncompressed AVI movies and then
converting them to h264 video using Handbrake (https://handbrake.fr/).  
I can't speak to codec details, but I've been pretty happy with this to
generate small movies that still look good.

Kurt

On 9/16/2014 6:01 AM, Guenter Giese wrote:

> Hi all,
>
> I want to generate movies for publication from neuronal structures
> recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image
> sequences are rather large up to GB), and movie size for publication
> is confined to 10 MB.
>
>
> Image sequence to video conversion (high compression): which software
> / codec do you recommend for preservation of small structures (cells,
> axons, dendrites)?
>
> Exact color rendition is not that critical (two-channel fluorescence
> images, plus labels in different colors).
>
> Freeware is preferred, or are there big advantages of commercial
> solutions?
>
> Thank you for recommendations!
>
> Guenter
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
Kurt Thorn
Director, Nikon Imaging Center
http://nic.ucsf.edu/blog/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Klaus Michel]

Hi Guenter,

I am using "XMedia Recode" (http://www.xmedia-recode.de/) to generate small movies
(Windows). I make an avi-file first and then convert and compress it with XMedia Recode.
Normally it is used to make movies playable on handheld devices and is specialized to
generate small movies. It offers a rich variety of codecs and parameters. You can use
"GSpot  " (http://gspot.headbands.com/) to identify the codecs that other people use. That
may help to find a promising codec for your purpose.

Best,

Klaus

On 9/16/2014 6:01 AM, Guenter Giese wrote:

> Hi all,
>
> I want to generate movies for publication from neuronal structures
> recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image
> sequences are rather large up to GB), and movie size for publication is
> confined to 10 MB.
>
>
> Image sequence to video conversion (high compression): which software /
> codec do you recommend for preservation of small structures (cells,
> axons, dendrites)?
>
> Exact color rendition is not that critical (two-channel fluorescence
> images, plus labels in different colors).
>
> Freeware is preferred, or are there big advantages of commercial
> solutions?
>
> Thank you for recommendations!
>
> Guenter
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Dr. Klaus Michel
Dept. of Human Biology Tel.: ++49 (0)8161 715079
TU München Fax: ++49 (0)8161 715785
Liesel-Beckmann-Strasse 4 email: [hidden email]
D-85350 Freising Weihenstephan


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[Peter Haub]

Hi Guenter,
have you thought about ffmpeg.
You can create a video from images with a command like:

ffmpeg -framerate 1/5 -i img%03d.png -c:v libx264 -r 30 -pix_fmt yuv420p out.mp4

Check
https://trac.ffmpeg.org/wiki/Create%20a%20video%20slideshow%20from%20images
regards
peter

On 16.09.2014 15:01, Guenter Giese wrote:

> Hi all,
>
> I want to generate movies for publication from neuronal structures
> recordings (TIFF image sequences 8bit greyscale, 24bit RGB). My image
> sequences are rather large up to GB), and movie size for publication
> is confined to 10 MB.
>
>
> Image sequence to video conversion (high compression): which software
> / codec do you recommend for preservation of small structures (cells,
> axons, dendrites)?
>
> Exact color rendition is not that critical (two-channel fluorescence
> images, plus labels in different colors).
>
> Freeware is preferred, or are there big advantages of commercial
> solutions?
>
> Thank you for recommendations!
>
> Guenter
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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