Save as video with auto contrast stacks?

Usage & Issues
#1

Hi everybody

I have a series of images in type 32-bit.
I choose Edit > Options > Appearance > Auto contrast stacks
The contrast of the images looks good in this way.
But I need to export this stacks as video with that contrast to present.
If I just save as AVI, the video shows the raw contrast of the images which is wrong.
I understand that the Auto contrast stacks did not change the value of the image itself.
I also tried to convert the images to 8-bit or RGB color, some of the pixel value lost
and the contrast shift a lot. So I prefer remain 32-bit.

How can I export image or video with specific brightness&contrast in fiji?
If not, is it possible to use python to solve this problem?

Thank you

#2

Hi,

can you explain why you want to change the contrast of every single image in the stack individually? For a stack or a movie (or anywhere where you show multiple images together) the brightness adjustement should be the same for all shown images.
If you face issues with bleaching etc., I’d rather recommend to do a bleaching correction first to correct the intensities.

To export as movie: I’m not so sure if 32bit is even possible for standard movie formats? In the end a movie is just a visualization which should run on any computer and nothing to extract measurements from so I’d recommend: analyze your image histogram (shortcut H, check whole stack), find the min or max (or something closeby ), then set these values manually in the Brightness&Contrast. then convert to 8bit (duplicate before!) and save as avi.
If you want other movie formats you need an external programme, e.g. ffmpeg.

If you want to keep the full information you can just save the tif stack.

#3

Hi,

Thank you for replying
The images came from an in situ experiment that the condition varies with different time. The video I want is just for visualization, not for analysis.
The problem is the max and min in B&C in each images is much different. for example: first image: 0.03~0.4 last image: 0.02~1.15.
If I set the min and max for one images, the other images in stacks will show too bright or dark.
If I choose auto contrast stack, the min and max will change depend the images(contain whole value) with similar brightness and contrast which is I want.

Also thanks for your advise,
If there is no other solution, I probably set the B&C value image by image, convert 8bit, combine as stack, and save as AVI.