I've been tried to align some histological slices on Amira but the software request a Stacked Slices file format.
The main problem that I don't possess the z-values of the slices. I saw a tutorial on Internet but it is not clear for me:
# Amira Stacked Slices
# Directory where image files reside pathname C:/data/pictures
# Pixel size in x- and y-direction pixelsize 0.1 0.1
# Image list with z-positions
picture1.tif 10.0
picture7.tif 30.0
picture13.tif 60.0
colstars.jpg 330.0
end
May I have to list all my 70 pictures? About the z-position, is it a random number?
Thank you
You can open the files without a .info file. Simply press "Open Data ...", select all the files, press "Open". You will then get a dialogue window where you might enter an arbitrary value for the (regular) z-distance. If you don't know the z-values, you might just leave it at 1.
That way you will create a data object of type "uniform coordinates" instead of "stacked slices".
Thank you! I will do this.
I have few slices and it is a kind of difficult to make a 3d model with few sections.
I'm still learning operate the amira 5.3 software
Hi there,
just an alternative way to try to figure it out. You may use Fiji or ImageJ free software to stack the individual images into a single stack. Provided that the images are immediately adjacent, you can import all these images into Fiji, for example using import raw command. To open multiple images from the same directory you can also use plugins-->macros-->record macro to prepare a ready command for file import. Next, change the names of individual slices to be imported in the code. Ultimately, go to image tab and choose stacks and then images to stack. When your stack is ready simply export it as stacked TIF or other format required and import it into the software you use. Hope this helps.
Best regards,
Adam
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