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Any compressed movie will be blurred to some degree. One of the reasons there is no standard algorithm is that the impact of any compression scheme will depend upon the nature of the image.
As was suggested, do retain the uncompressed file(s). If you need to edit the movie, make the changes on a copy of the uncompressed file. Re-editing the the compressed version will often turn it to mush.
thanks to all who made suggestions for movie making tools.
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923 USA
(206) 616-4156
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On Mar 1, 2013, at 4:26 AM, simon walker <[log in to unmask]> wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
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>
> Thanks for all the suggestions with this. If nothing else, this has shown that there are many options and no accepted standard. Maybe it's time for a recognised standard method of compression for use with fluorescence microscopy data. It would be useful if there were an option available in ImageJ/FIJI to implement this. In the meantime we have managed to shrink our movie files using Adobe Media Encoder into MP4 format using H.264. The result is a little blurry, but the file size is ~10 fold smaller and it's still possible to see what we're trying to show. As suggested we'll upload the raw data somewhere for reviewers to access if required.
> Simon
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[log in to unmask]] On Behalf Of Cameron Nowell
> Sent: 28 February 2013 23:50
> To: [log in to unmask]
> Subject: Re: Video compression
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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>
> Hi All,
>
> I routinely use Handbrake (http://handbrake.fr/) its open source and quite easy to use. With handbrake installed and the latest FFDShow codec packs (http://ffdshow-tryout.sourceforge.net/) you have a lot of power at your fingertips to compress to any format you want.
>
>
> Cheers
>
> Cam
>
>
>
> Cameron J. Nowell
> Centre for Dynamic Imaging
> The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, Victoria 3052 Australia
>
> Phone: +61 3 9345 2871
> Mobile: +61422882700
> Fax: +61 3 9347 0852
>
> Facility Website
> LinkedIn Profile
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[log in to unmask]] On Behalf Of Mario Emmenlauer
> Sent: Friday, 1 March 2013 3:18 AM
> To: [log in to unmask]
> Subject: Re: Video compression
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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>
> Hi,
>
> we used several different of the newer video compression codecs, like XviD or DivX and Quicktime, they all give surprisingly good results if you don't have too much noise. You can prefilter a bit to reduce noise and improve compression further.
>
> With XviD we often compress 500MB TIFF time series of 2MP to ~10MB, with acceptable quality, good enough for Beamer presentation. Thats of course all depending on your noise and variance between images, but I would anticipate a 10 - 50 fold decrease of size. XviD is well sup- ported and freeware on most platforms, and we export from MetaXpress directly.
>
> Best,
>
> Mario
>
>
>
>
> On 02/27/2013 05:08 PM, John Oreopoulos wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> I use the same method described by Jay below. This works very well for me.
>>
>> John Oreopoulos
>>
>>
>> On 2013-02-27, at 11:05 AM, "Unruh, Jay" <[log in to unmask]> wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
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>>> *****
>>>
>>> The size limits for publication are unfortunate. You essentially have no choice but to reduce the quality of movies so you can publish them. I suppose the purpose of this is for rapid web viewing.
>>>
>>> We routinely use Quicktime Pro (no commercial connection) with the H.264 compression (also low cost software at around $30). It does a relatively decent job of compressing and preserving sharp features and gives you flexibility on compression level. My typical workflow is to convert to RGB and then save as uncompressed avi from ImageJ. Those movies will import directly into Quicktime Pro.
>>>
>>> I would also highly recommend providing uncompressed or even raw files via your own website so people can access them there. I have seen situations where authors reference the website from within a publication to direct people there (http://www.nature.com/nature/journal/v466/n7305/full/nature09255.html).
>>>
>>> Jay
>>>
>>> -----Original Message-----
>>> From: Confocal Microscopy List
>>> [mailto:[log in to unmask]] On Behalf Of Guy Cox
>>> Sent: Wednesday, February 27, 2013 6:56 AM
>>> To: [log in to unmask]
>>> Subject: Re: Video compression
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Jasc Software Paint Shop Pro also comes with Animation Shop which offers a wide range of compression options. Some are terrible, others are good - it needs a fair bit of experimentation. But it is low cost software. I use it a lot, but otherwise have no commercial connection.
>>>
>>> Guy
>>>
>>> -----Original Message-----
>>> From: Confocal Microscopy List
>>> [mailto:[log in to unmask]] On Behalf Of Simon Walker
>>> Sent: Wednesday, 27 February 2013 11:06 PM
>>> To: [log in to unmask]
>>> Subject: Video compression
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Dear List,
>>> Can anyone recommend software for video compression (either free or licensed)? We have some large files from live cell imaging exps that we need to submit to a journal and somehow get them down to less than 10 MB (this size limit seems crazy in this day and age, but maybe there are still people using dial-up to access journals..). What codecs/file formats are people using to obtain the best compression with minimal loss of information?
>>> Thanks,
>>> Simon
>>
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