What kind of analysis are you doing with ImageJ?. If it is something relative simple maybe you can use Matlab. They have very strong image processing tools.

So maybe a solution is to do all the analysis in Matlab. You make a code to read video, extract the frames and do the processing there.

Now you are doing a lot of work manually, Good luck

Dear Bishwarup,

I would convert your video into single frame images (there a plenty of youtube videos that explain that and a whole bunch of software options) You might not need every frame so may be check out that video (https://www.youtube.com/watch?v=q1_oZq8LGY8).

Than you can load them into imageJ as Stack using the File->Import -> Image sequence function. If the file will be too big you might think about a virtual stack, of leaving out some images by changing the image increment number.

Best Soenke

If it helps anyone - "ispy" software will record, on a webcam, in an appropriate format (uncompressed avi) to open in ImageJ. I had a nightmare tring to convert a test video from QuickTime format and various other formats to uncompressed avi, although some people say that this can be done in the open source software "VirtualDub".

Sorry for posting the answer so late. I found the solution in using ffmpeg to convert my videos. I convert my clips into uncompressed avi files using ffmpeg and they work perfectly in ImageJ.

For everyone who does not know how to use ffmpeg, having the same troubles I had, here is a great guide explaining all the steps from the beginning: http://www.hongkiat.com/blog/ffmpeg-guide/

You will need this code for converting into an uncompressed avi working in ImageJ: "ffmpeg -i input.mts -an -vcodec rawvideo -y output.avi"  There is a limitation on the file size. Good luck!

If you have several videos to convert, run

$ for f in *.MTS; do ffmpeg -i $f -an -vcodec rawvideo -y ${f%.*}.avi; done

in your Linux shell (Windows users might need to adapt this script). This will convert each .MTS in the current directory into a .avi of the same name keeping high quality.

-- alternative to raw, smaller files --

Had the same struggle, finally downloaded ffmpeg as I could not get the VLC route going. The Win64 zip just needs to be unpacked and if you place the video to convert in the bin-folder of ffmpeg then command line options can be used like in the posts of Nathalie and Rachel.

The raw option gives super huge videos, but the following settings work with all kind of videos I tried so far:

In essence, change encoding from rawvideo to mjpeg and quality can be adapted with -q:v # where # is a number, 0=no compression, higher numbers give smaller files but with artifacts.

examples

---video saved from a PPT as mov and converted...

ffmpeg -i Media1.mov -an -vcodec rawvideo -y output.avi (1.2 GB !!)

ffmpeg -i Media1.mov -an -c:v mjpeg -y output_mjpeg.avi (16 MB big) ... quality not too good

ffmpeg -i Media1.mov -an -c:v mjpeg -q:v 0 -y output3_qv0.avi (56 MB big) ... q:v 0 = max quality

ffmpeg -i Media1.mov -an -c:v mjpeg -q:v 2 -y output4_qv0.avi (56 MB big) ... optically same quality

ffmpeg -i Media1.mov -an -c:v mjpeg -q:v 10 -y output4_qv10.avi (28 MB big) ... quality not as good, but ok

---Videos from mobile phone

ffmpeg -i X384.mp4 -an -c:v mjpeg -q:v 2 -y X384.avi

... mp4 84MB, avi 296MB and some warnings during conversion, looks ok and but can be opened in imageJ

ffmpeg -i X384.mp4 -an -c:v mjpeg -q:v 5 -y X384_q5.avi

... mp4 84MB, avi 155MB and some warnings during conversion, looks ok and but can be opened in imageJ

ffmpeg -i X384.mp4 -an -c:v mjpeg -q:v 10 -y X384_q10.avi

... mp4 84MB, avi 106MB and some warnings during conversion, looks ok and but can be opened in imageJ

--- Zwick Videos

ffmpeg -i V_XX_1.wmv -an -c:v mjpeg -q:v 10 -y V_XX_1.avi

... wmv 34MB, according to vlc framerate 25, total time 54s

... avi 17MB can be opened in imageJ, framerate 11.083 fps, total time 55.04s

ffmpeg -i V_XX_1.wmv -an -c:v mjpeg -q:v 2.0 -y V_XX_1_q2p0.avi

... wmv 34MB, according to vlc framerate 25, total time 54s

... avi 39MB, can be opened in imageJ, framerate 11.083 fps, total time 55.04s

To convert videos to import in imagej I am using the http:\\openshot.org video editor. Openshot is open source, it imports quite a few formats and it has an option to export the video as png image sequence. See screenshot of the advanced export dialog.

After the images are exported they can be imported into imagej (File>Import>Image Sequence)

I use AVC (Any video converter) to convert any kind of video file to FFmpeg, avi

AVC (Any video converter) did the trick and was free and easy

For those who know basic python and can run a simple python script, here is a code to get uncompressed avi video for ImageJ which worked fine for me (Note: it will convert RGB video(any format) to greyscale(uncompressed avi) & It also works fine if the example video is already Black & white). Save the file in the same folder where the example video is saved and rename the "your_video.mp4" in code to your reference video name and run it. the output file will be saved in the same folder.

Thanks ;)

import numpy as np import cv2

#Chnage your video file name here cap = cv2.VideoCapture('your_video.mp4') ret, frame = cap.read() print('ret =', ret, 'W =', frame.shape[1], 'H =', frame.shape[0], 'channel =', frame.shape[2]) FPS= 20.0 FrameSize=(frame.shape[1], frame.shape[0]) fourcc = cv2.VideoWriter_fourcc(*'MJPG') out = cv2.VideoWriter('Video_output.avi', fourcc, FPS, FrameSize, 0) while(cap.isOpened()): ret, frame = cap.read() # check for successfulness of cap.read() if not ret: break gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY) frame = gray # Save the video out.write(frame) cv2.imshow('frame',frame) if cv2.waitKey(1) & 0xFF == ord('q'): break cap.release() out.release() cv2.destroyAllWindows()

For those who converted the video using AVC, I can not find the FFmpeg avi type, could you please be more specific? Thank you.

Unfortunately, the top answer ("most recommended," from Nathalie Maria Malewicz in 2017) has broken links....

To open .avi files in Fiji, first go to Help and then update. After completing the updates, a dialog box opens. In that, go to manage update sites and tick on the box corresponding to FFmpeg, close it and then apply changes. Once this is done the software asks for restart. After restarting, once again run the updates. Now to open .avi files: Go to File; Import; movie (ffmpeg) and select the required file. Also, remember to untick the virtual stack box.

In case somebody needs to split a video into images (substitute mp4 and bmp with what is appropriate):

ffmpeg -i .mp4 %04d.bmp

If, besides, you need to convert to greyscale:

ffmpeg -i .mp4 -vf hue=s=0 %04d.bmp