Hello,
I would like to use Neuron Studio in order to quantify dendrite and spine morphological features in 200 um brain sections stained with Golgi-Cox.
Neuron Studio software opens TIFF stacks derived from ND2 format through ImageJ Plug-in conversion, but doesn't trace any neurite when asked to, I think because of an apparent resolution drop (the TIFF stack looks the same as ND2 when in ImageJ, but looks low quality when in Neuron Studio).
Did anybody encounter this problem before and knows how to solve it?
Thank you in advance.
P.S. These are two examples of what I see in ImageJ (1) and in Neuron Studio (2) for the same stack.
Dear Julia,
I'm not extremely familiar with Neuron Studio but I do not know if I would describe the difference between the two images as a drop in resolution.
The two images look significantly different: it looks like the darkest structures in the ImageJ picture are completely absent in the second image, while some of the originally dim structures are highlighted. Could this be a mistake in translating an RGB figure into grey scale? For example, imagine that you give Neuron Studio a RGB picture, and the later only loads one of the color channels in an attempt to obtain a gray scale. If you R G and B channels are not exactly the same then you will loose information, which would translate in loosing some of the original structures you could see on image J.
Best,
Dear Giulia,
I also don't know about your software, but I suggest that you contact the Technical help for Neuron Studio. To me, it looks like it has changed the LUT for the grayscale, or flattened or clipped the histogram. I also think that the resolution is the same, but now all of the Golgi-stained parts of the neuron are of a similar grey value. Perhaps the software does this as a way to collapse the 3D depth to 2D for tracing?
Of course, I am just going by the JPGs you posted, and am not sure what your original TIFFs look like.
Best,
Jill
Thank you everybody :)
Rafael Camacho, you're right, there should be a problem with the distribution of information among channels that the TIFF conversion makes evident. The picture is taken in brightfield with a black staining, so it comes out as b/w. I'll try to see if the acquisition default mode is correct.
Jill Miotke, Neuron Studio should be suited to analyze only 3D stacks, so I don't think that the problem is the result of a collapsing procedure, but it does seem that the TIFF reader and converter in ImageJ is not suited for the kind of stacks I am using it for, so that after the conversion something is missing.
Dear Guilia,
To me it looks like to different slices of the stack, the one in image J in focus and the one in Neuron Studio slightly out of focus. When you import the picture series, does Neuron Studio transform the stack into an overlay? If not, can you go through the stack picture by picture to find a slice that also is in focus so you can run the analysis of dendrites and spines? If you have an overlay in Neuron Studio, reduce the stack before importing it. You can do this in ImageJ, just remove a couple of slices in the beginning and the end of your stack. Or just pick single slices from the stack for analysis.
Good luck! Cheers,
Tilo
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