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tractatus / wholebrain

R package for segmentation, registration and generating web-based brain atlases from microscope images
GNU General Public License v3.0
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problems with the segmetation command #12

Open bex605 opened 5 years ago

bex605 commented 5 years ago

hi daniel!

first of all i really like your idea of wholebrain and i would love to work with it! however i'm having some troubles using it. so far we only managed to install it on one computer only, which is a linux. but there it works fine so this is ok for now. my main problem at the moment is the segmentation function. i can use the command "segment(xy)", my image, the controls (like 8-bit render, eccentricity, etc) and the histogram open up. but this is where i'm struggeling:

1) for the 8-bit render i have to use the smallest setting (like 0-225) to actually see something - and it's still pretty dark. this also counts for the intensity setting, to set which dots are indeed cells and which are not. this makes it really hard to vary the scales to find the optimal setting.

2) the brain outline keeps disappearing. usually it appears when i open the image. but as soon as i change any of the settings, it disappears. sometimes it comes back for a second, sometimes it doesn't. additionally it doesn't encircle the whole brain, but always leaves a small spot open at the edge. the lines of the brain outline not only leave the brain "open", but they "shoot" to the edge of the image in a straight line.

i've attached two pictures (i hope this works..) which might give you an idea about my problems with the control settings and the brain outline. i'd really appreciate your help.

best regards, rebecca

settings brain outline

metracy commented 5 years ago

I think this is because you're working with a non 16bit greyscale image. I had the same issue and it required using photoshop to be able to save things as 16bit greyscale.

bex605 commented 5 years ago

I think this is because you're working with a non 16bit greyscale image. I had the same issue and it required using photoshop to be able to save things as 16bit greyscale.

thanks for your response!!

I took the images with the Leica Software LASX. Hence they were first saved as "lif" files. There is an option in LASX to export the images to tif files - even with the option "without any data compression". However I don't know if this means, that the images are saved as 16-bit images.

Can I convert lif files to 16bit tif files with photoshop? and are there any other programs, which could do that?

tractatus commented 5 years ago

@bex605 on the Leica microscope just export as 16 bit TIFF and you will be good to go. your brain is upside down so you might want to fix that as well.