Calcium imaging- avi analysis

[Ron Feiner]

Hey,
I've been taking videos of calcium imgaing in caardiomyocytes and am trying to analyse the movies using ImageJ. The movies are 100fps and are rather heavy so when I try opening them only 200 frames open but not the first 200 but rather all the frames are jammed into 200 frames which makes the movie run very fast and distorts my data. When I try to open the movie as a virtual stack i get an error saying "chunk size too short" and I cannot open a compressed version of the movie.
Can anyone help me import the movie in regular speed?
Thank you,
Ron Feiner

[Michael Schmid]

Hi Ron and everyone,

this problem is solved in today's daily build of ImageJ (Help>Update ImageJ, select 'daily build from the drop-down menu).
The problem was due to a movie type with blank frames (possibly lost frames because the computer was too slow to record the full frame rate).

Restrictions when importing movies with blank frames:

- ImageJ now only shows the non-blank frames; the stack therefore has fewer stacks than the movie (when also counting the blank frames).
- Time in the slice info is correct only when opening the .avi as virtual stack. Upon writing the data into an avi file again, the original time information will be lost in any case.
- Selection of start and end frames is inconsistent between normal and virtual stacks: when opening the .avi as a normal stack, only the non-blank frames are counted; when opening as a virtual stack, all frames are counted (nevertheless, only non-blank frames will be displayed).
- Blank frames with AVI-type 1 index probably still does not work (I have not seen such a file to try)


Michael
________________________________________________________________
On Dec 1, 2012, at 14:27, Ron Feiner wrote:

> Hey,
> I've been taking videos of calcium imgaing in caardiomyocytes and am
> trying to analyse the movies using ImageJ. The movies are 100fps and
> are rather heavy so when I try opening them only 200 frames open but
> not the first 200 but rather all the frames are jammed into 200 frames
> which makes the movie run very fast and distorts my data. When I try
> to open the movie as a virtual stack i get an error saying "chunk size
> too short" and I cannot open a compressed version of the movie.
> Can anyone help me import the movie in regular speed?
> Thank you,
> Ron Feiner

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

[Kenton Arkill]

Dear All

I'm writing a macro to find the directionality of particles and the plugin works very well, but is there a way of extracting the outputs (direction and dispersion) in the macro language so I can do thousands?
Regards
Kenton

On 7 Dec 2012, at 09:06, Michael Schmid wrote:

> Hi Ron and everyone,
>
> this problem is solved in today's daily build of ImageJ (Help>Update ImageJ, select 'daily build from the drop-down menu).
> The problem was due to a movie type with blank frames (possibly lost frames because the computer was too slow to record the full frame rate).
>
> Restrictions when importing movies with blank frames:
>
> - ImageJ now only shows the non-blank frames; the stack therefore has fewer stacks than the movie (when also counting the blank frames).
> - Time in the slice info is correct only when opening the .avi as virtual stack. Upon writing the data into an avi file again, the original time information will be lost in any case.
> - Selection of start and end frames is inconsistent between normal and virtual stacks: when opening the .avi as a normal stack, only the non-blank frames are counted; when opening as a virtual stack, all frames are counted (nevertheless, only non-blank frames will be displayed).
> - Blank frames with AVI-type 1 index probably still does not work (I have not seen such a file to try)
>
>
> Michael
> ________________________________________________________________
> On Dec 1, 2012, at 14:27, Ron Feiner wrote:
>
>> Hey,
>> I've been taking videos of calcium imgaing in caardiomyocytes and am
>> trying to analyse the movies using ImageJ. The movies are 100fps and
>> are rather heavy so when I try opening them only 200 frames open but
>> not the first 200 but rather all the frames are jammed into 200 frames
>> which makes the movie run very fast and distorts my data. When I try
>> to open the movie as a virtual stack i get an error saying "chunk size
>> too short" and I cannot open a compressed version of the movie.
>> Can anyone help me import the movie in regular speed?
>> Thank you,
>> Ron Feiner
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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