importing video in image J
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Hello,
I would like to import a video file in Fiji/imageJ in order to track mice. I tried different video formats with several converters like : - .avi : The following message appears : "An error occurred reading the AVI file, unsupported compression : 34363248 'H264' " or even "Not an avi file" with an other converter. - .mov with QuickTime 7 Pro : I have a frame named "Bioformats import option", and when I click on "Ok", I have the following message "File is not a supported format, a reader plugin is not availaible, or it was not found". And howerver, I have the plugin "QT_Movie_Opener", "QT_Stack_Writer" and "QTVirtualStack". I also tried the solutions offered in this image J listserv like : -using FFMPEG (free video conversion software) but I can't load it -trying the FFMPEG plugin but it didn't change anything -using virtualdub and then exporting as a bmp stack then ImageJ/Fiji, but I can't open all the fragmented images in image J, I can only import them one by one Do you have any solution/suggestions to my problem to import a video in image J/Fiji ? It would be very helpful, Thank you, Julie -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: importing video in image J
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As I've posted in the past, we use Quicktime Pro to output the movies to folders of single frame images. The software has options for a few formats and different fame sampling rates. We've used this for many formats including a project where someone used an iPhone to take 10 minute movies of mice in a box.
========================================================================= Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center Cell: 914-309-3270 ** MY OFFICE HAS MOVED TO SKIRBALL 2nd FLOOR, Back right ** http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jouan Julie Sent: Thursday, June 11, 2015 10:50 AM To: [hidden email] Subject: importing video in image J Hello, I would like to import a video file in Fiji/imageJ in order to track mice. I tried different video formats with several converters like : - .avi : The following message appears : "An error occurred reading the AVI file, unsupported compression : 34363248 'H264' " or even "Not an avi file" with an other converter. - .mov with QuickTime 7 Pro : I have a frame named "Bioformats import option", and when I click on "Ok", I have the following message "File is not a supported format, a reader plugin is not availaible, or it was not found". And howerver, I have the plugin "QT_Movie_Opener", "QT_Stack_Writer" and "QTVirtualStack". I also tried the solutions offered in this image J listserv like : -using FFMPEG (free video conversion software) but I can't load it -trying the FFMPEG plugin but it didn't change anything -using virtualdub and then exporting as a bmp stack then ImageJ/Fiji, but I can't open all the fragmented images in image J, I can only import them one by one Do you have any solution/suggestions to my problem to import a video in image J/Fiji ? It would be very helpful, Thank you, Julie -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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I also use Quicktime Pro (version 7 as the later ones don’t have many features). I output tiff sequences from Fiji and then import the image sequence into Quicktime Pro so I can export as a movie using any of the codecs Apple offers. Dave
On Jun 11, 2015, at 12:48 PM, Cammer, Michael <[hidden email]<mailto:[hidden email]>> wrote: As I've posted in the past, we use Quicktime Pro to output the movies to folders of single frame images. The software has options for a few formats and different fame sampling rates. We've used this for many formats including a project where someone used an iPhone to take 10 minute movies of mice in a box. ========================================================================= Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center Cell: 914-309-3270 ** MY OFFICE HAS MOVED TO SKIRBALL 2nd FLOOR, Back right ** http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jouan Julie Sent: Thursday, June 11, 2015 10:50 AM To: [hidden email]<mailto:[hidden email]> Subject: importing video in image J Hello, I would like to import a video file in Fiji/imageJ in order to track mice. I tried different video formats with several converters like : - .avi : The following message appears : "An error occurred reading the AVI file, unsupported compression : 34363248 'H264' " or even "Not an avi file" with an other converter. - .mov with QuickTime 7 Pro : I have a frame named "Bioformats import option", and when I click on "Ok", I have the following message "File is not a supported format, a reader plugin is not availaible, or it was not found". And howerver, I have the plugin "QT_Movie_Opener", "QT_Stack_Writer" and "QTVirtualStack". I also tried the solutions offered in this image J listserv like : -using FFMPEG (free video conversion software) but I can't load it -trying the FFMPEG plugin but it didn't change anything -using virtualdub and then exporting as a bmp stack then ImageJ/Fiji, but I can't open all the fragmented images in image J, I can only import them one by one Do you have any solution/suggestions to my problem to import a video in image J/Fiji ? It would be very helpful, Thank you, Julie -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- 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 91 N. Eagleville Rd. Storrs, CT 06269 860-486-2200 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: importing video in image J
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In reply to this post by Jouan Julie
Hi Julie,
well, ffmpeg should work for an H264 movie, e.g. ffmpeg -i infile.avi -pix_fmt nv12 -f avi -vcodec rawvideo outfile.avi This creates an NV12-coded avi file which can be opened by ImageJ. NV12 causes no compression losses in addition to those caused by H264 compression already. You can also convert the movie with Virtualdub into an AVI with raw format. Select Uncompressed RGB/YCbCr as compression. If you decompress the movie into single files, this should also work. Use File>Import>Image Sequence to open all files as a stack in ImageJ. Michael __________________________________________________________________ On Thu, June 11, 2015 16:49, Jouan Julie wrote: > Hello, > > I would like to import a video file in Fiji/imageJ in order to track mice. > I tried different video formats with several converters like : > > - .avi : The following message appears : "An error occurred reading the > AVI file, unsupported compression : 34363248 'H264' " or even "Not an avi > file" with an other converter. > > - .mov with QuickTime 7 Pro : I have a frame named "Bioformats import > option", and when I click on "Ok", I have the following message "File is > not a supported format, a reader plugin is not availaible, or it was not > found". And howerver, I have the plugin "QT_Movie_Opener", > "QT_Stack_Writer" and "QTVirtualStack". > > I also tried the solutions offered in this image J listserv like : > > -using FFMPEG (free video conversion software) but I can't load it > -trying the FFMPEG plugin but it didn't change anything > -using virtualdub and then exporting as a bmp stack then ImageJ/Fiji, but > I can't open all the fragmented images in image J, I can only import them > one by one > > Do you have any solution/suggestions to my problem to import a video in > image J/Fiji ? > It would be very helpful, > > Thank you, > Julie -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Knecht, David
Hello,
I use VirtualDub, export each image into a folder (.jpg) and import them as image sequence in ImageJ. You can then save it as avi. I also track cells using TrackMate so I just use the image sequence file to track. I have been using the method for the last 2 years so I am quite sure it works. :) Cheers, Karen ᐧ On Thu, Jun 11, 2015 at 6:55 PM, Knecht, David <[hidden email]> wrote: > I also use Quicktime Pro (version 7 as the later ones don’t have many > features). I output tiff sequences from Fiji and then import the image > sequence into Quicktime Pro so I can export as a movie using any of the > codecs Apple offers. Dave > > On Jun 11, 2015, at 12:48 PM, Cammer, Michael <[hidden email] > <mailto:[hidden email]>> wrote: > > As I've posted in the past, we use Quicktime Pro to output the movies to > folders of single frame images. The software has options for a few formats > and different fame sampling rates. We've used this for many formats > including a project where someone used an iPhone to take 10 minute movies > of mice in a box. > > ========================================================================= > Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical > Center > Cell: 914-309-3270 ** MY OFFICE HAS MOVED TO > SKIRBALL 2nd FLOOR, Back right ** > http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/ > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Jouan Julie > Sent: Thursday, June 11, 2015 10:50 AM > To: [hidden email]<mailto:[hidden email]> > Subject: importing video in image J > > Hello, > > I would like to import a video file in Fiji/imageJ in order to track mice. > I tried different video formats with several converters like : > > - .avi : The following message appears : "An error occurred reading the > AVI file, unsupported compression : 34363248 'H264' " or even "Not an avi > file" with an other converter. > > - .mov with QuickTime 7 Pro : I have a frame named "Bioformats import > option", and when I click on "Ok", I have the following message "File is > not a supported format, a reader plugin is not availaible, or it was not > found". And howerver, I have the plugin "QT_Movie_Opener", > "QT_Stack_Writer" and "QTVirtualStack". > > I also tried the solutions offered in this image J listserv like : > > -using FFMPEG (free video conversion software) but I can't load it -trying > the FFMPEG plugin but it didn't change anything -using virtualdub and then > exporting as a bmp stack then ImageJ/Fiji, but I can't open all the > fragmented images in image J, I can only import them one by one > > Do you have any solution/suggestions to my problem to import a video in > image J/Fiji ? > It would be very helpful, > > Thank you, > Julie > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > 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 > 91 N. Eagleville Rd. > Storrs, CT 06269 > 860-486-2200 > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- *Karen Grace V. Bondoc | Ph.D. Student* *International Max Planck Research School * *Institute for Inorganic and Analytical Chemistry * *Bioorganic Analytics, Friedrich-Schiller-Universität Jena* *Lessingstr. 8 (R 228)* *D-07743 Jena* *Tel.: 03641 948956* -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thank you for your help !
Best, Julie > Message du 12/06/15 13:23 > De : "Karen Grace Bondoc (UNIJENA)" > A : [hidden email] > Copie à : > Objet : Re: importing video in image J > > Hello, > I use VirtualDub, export each image into a folder (.jpg) and import them as > image sequence in ImageJ. You can then save it as avi. I also track cells > using TrackMate so I just use the image sequence file to track. I have been > using the method for the last 2 years so I am quite sure it works. :) > > Cheers, > Karen > > > ᐧ > > On Thu, Jun 11, 2015 at 6:55 PM, Knecht, David > wrote: > > > I also use Quicktime Pro (version 7 as the later ones don’t have many > > features). I output tiff sequences from Fiji and then import the image > > sequence into Quicktime Pro so I can export as a movie using any of the > > codecs Apple offers. Dave > > > > On Jun 11, 2015, at 12:48 PM, Cammer, Michael > > wrote: > > > > As I've posted in the past, we use Quicktime Pro to output the movies to > > folders of single frame images. The software has options for a few formats > > and different fame sampling rates. We've used this for many formats > > including a project where someone used an iPhone to take 10 minute movies > > of mice in a box. > > > > ========================================================================= > > Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical > > Center > > Cell: 914-309-3270 ** MY OFFICE HAS MOVED TO > > SKIRBALL 2nd FLOOR, Back right ** > > http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/ > > > > > > -----Original Message----- > > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > > Jouan Julie > > Sent: Thursday, June 11, 2015 10:50 AM > > To: [hidden email] > > Subject: importing video in image J > > > > Hello, > > > > I would like to import a video file in Fiji/imageJ in order to track mice. > > I tried different video formats with several converters like : > > > > - .avi : The following message appears : "An error occurred reading the > > AVI file, unsupported compression : 34363248 'H264' " or even "Not an avi > > file" with an other converter. > > > > - .mov with QuickTime 7 Pro : I have a frame named "Bioformats import > > option", and when I click on "Ok", I have the following message "File is > > not a supported format, a reader plugin is not availaible, or it was not > > found". And howerver, I have the plugin "QT_Movie_Opener", > > "QT_Stack_Writer" and "QTVirtualStack". > > > > I also tried the solutions offered in this image J listserv like : > > > > -using FFMPEG (free video conversion software) but I can't load it -trying > > the FFMPEG plugin but it didn't change anything -using virtualdub and then > > exporting as a bmp stack then ImageJ/Fiji, but I can't open all the > > fragmented images in image J, I can only import them one by one > > > > Do you have any solution/suggestions to my problem to import a video in > > image J/Fiji ? > > It would be very helpful, > > > > Thank you, > > Julie > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > > 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 > > 91 N. Eagleville Rd. > > Storrs, CT 06269 > > 860-486-2200 > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > *Karen Grace V. Bondoc | Ph.D. Student* > *International Max Planck Research School * > *Institute for Inorganic and Analytical Chemistry * > *Bioorganic Analytics, Friedrich-Schiller-Universität Jena* > *Lessingstr. 8 (R 228)* > *D-07743 Jena* > > *Tel.: 03641 948956* > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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