Importing MP4 video in FIJI for analysis on each frame

Usage & Issues
#1

I’m trying to import multiple MP4 files from a microscope camera. The video files are shot at 60 fps with 1080p resolution. When I import and save these videos in FIJI using the ffmpeg plugin, the resulting file size gets prohibitively large and the software hangs up (I’m saving them in TIFF or AVI). Here’s the Dropbox link to one of the MP4 files.

Dendrite Growth

The video shows a dendrite growing between two pointed electrodes, I want to calculate the area of dendrite in each frame to quantify the areal growth of the dendrite with time.

How do I go about importing the files? For the analysis, I’m planning to crop the video to only have the strip of electrolyte where the dendrite is growing and then use thresholding to select the dendrite area in each frame. If you have a better idea about how to analyse the video to get dendrite area with time, I’d appreciate that as well.

Thank you!

#2

Hi,

I tried to import your movie file on ImageJ by own plugin.
This plugin use ffmpeg(javacv), so I think it is same method compare with the ffmpeg plugin.
The loaded image size is about 8GB…(*in the case of ffmpeg plugin, using virtual stack, 40GB over… )
So, if your Fiji can’t set the memory size over 8GB, it should hang up.
And I developed another plugin which can convert movie file to sequential tiff files without display.
If you need these plugins, I would like to upload them on our website.

hwada

#3

Hello again hwada,
If you don’t mind, even if they can’t use it I’m sure that I could. Would you mind setting it up please?
Bob

#4

Hi Bob,

O.K, I will upload them as soon as possible.

hwada

#5

Hi again,

I uploaded them on our website.
Please download and try them.

MovieLoader
and
MovieToTiff

#6

Maybe the problem is caused by the file format? Try converting the video https://www.videoconverter.com/how-to-convert-mp4-to-mov.html.

#7

wow, just spent 10 min on your website and could not figure out how to install JavaCV into FIJI as a jar. if your movieloader works, could you possibly post instructions? it sounds very useful, but i can’t fathom your website

#8

The version of JavaCV in fiji is 1.4, and the structure has changed since 1.5, and some plugins do not support this, so they may not work.
My plugin is coded using the 1.5 system, so it need to install the 1.5.* .
However, it cannot live with the 1.4 system, so you need to choose one of them.
In addition, only the necessary JavaCV packages are installed in Fiji.
Therefore, when replacing them manually, you need to move or delete the corresponding jar files, which is quite complicated.
For now, if you want to use my plug-in, you can use ImageJ and install the latest version of JavaCV.
However, I have confirmed that my plugin works up to 1.54.

Select javacv-platform-***-bin.zip from Download in JavaCV site.
After unzipping, copy this directory to the ImageJ plugins directory.

hwada

#9

I’m sorry, I misunderstood.
The plugin SaveMov does what I just described, but I’ve seen it work from 1.41 to 1.54 with this plugin.