help > Color tracing
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Oct 3, 2016 03:10 PM | Manuel FOSSA - M2C
Color tracing
Dear all,
First i must say that i'm a new user of Vaa3D (great software!) and that i use it not for neuroinformatics at all but in the contexte of hydro-climatology!
Let me introduce my data set: It is a 4D TIF stack with 3 independent variables: X and Y are spatial dimensions Z is a time dimension . The dependent variable (let's call it C) is a measure of curvature.
The data can be seen as a time series of X*Y curvature scalars. Let's say positive curvature points are yellow and negative are blue. What i would like to do is to trace lines of similar curvature across the XYZ dimensions. This means i would like to detect if lines of constant curvature thus constant color exist in the space-time domain.
Looking at the examples of neuron tracing i think something similar for my application would be possible with Vaa3D.
Do you think it can be done? If yes, how?
Thank you very much!
First i must say that i'm a new user of Vaa3D (great software!) and that i use it not for neuroinformatics at all but in the contexte of hydro-climatology!
Let me introduce my data set: It is a 4D TIF stack with 3 independent variables: X and Y are spatial dimensions Z is a time dimension . The dependent variable (let's call it C) is a measure of curvature.
The data can be seen as a time series of X*Y curvature scalars. Let's say positive curvature points are yellow and negative are blue. What i would like to do is to trace lines of similar curvature across the XYZ dimensions. This means i would like to detect if lines of constant curvature thus constant color exist in the space-time domain.
Looking at the examples of neuron tracing i think something similar for my application would be possible with Vaa3D.
Do you think it can be done? If yes, how?
Thank you very much!
Oct 3, 2016 04:10 PM | Zhi Zhou
RE: Color tracing
For color separation, you can use our color separator plugin under
"Plug-In" --> "neuron_utilities" --> "neuron_color_separator"
to separate different colors.
For curvature detection, you can use try different neuron tracing plugins under "Plug-In" --> "neuron_tracing" menu to find an optimal one for your data.
For curvature detection, you can use try different neuron tracing plugins under "Plug-In" --> "neuron_tracing" menu to find an optimal one for your data.
Oct 4, 2016 01:10 PM | Manuel FOSSA - M2C
RE: Color tracing
Dear Zhi,
Thanks for your answer. Is there any documentation on how to use both plugins? I don't known how to use the color separator and of the neuron tracing plug ins i've watched the neuron tracing 1.0 and 2.0 videos but both seems to require that either you landmark the begining and end of you neuron or paint it which is obviously where is my difficulty: it is very hard the visually detect it so i'd like to make it automatic (especially in cross XY-Z directions)
Thanks for your answer. Is there any documentation on how to use both plugins? I don't known how to use the color separator and of the neuron tracing plug ins i've watched the neuron tracing 1.0 and 2.0 videos but both seems to require that either you landmark the begining and end of you neuron or paint it which is obviously where is my difficulty: it is very hard the visually detect it so i'd like to make it automatic (especially in cross XY-Z directions)
Oct 4, 2016 03:10 PM | Hanchuan Peng
RE: Color tracing
The color separation has not been
published yet so we do not have a formal document on it, however it
is quite easy to use, just following the GUI dialog.
If you have difficulty to use Vaa3D Neuron 1 or Neuron 2, try to attach a sample image so we can take a look when we find time.
-Hanchuan
Originally posted by Manuel FOSSA:
If you have difficulty to use Vaa3D Neuron 1 or Neuron 2, try to attach a sample image so we can take a look when we find time.
-Hanchuan
Originally posted by Manuel FOSSA:
Dear Zhi,
Thanks for your answer. Is there any documentation on how to use both plugins? I don't known how to use the color separator and of the neuron tracing plug ins i've watched the neuron tracing 1.0 and 2.0 videos but both seems to require that either you landmark the begining and end of you neuron or paint it which is obviously where is my difficulty: it is very hard the visually detect it so i'd like to make it automatic (especially in cross XY-Z directions)
Thanks for your answer. Is there any documentation on how to use both plugins? I don't known how to use the color separator and of the neuron tracing plug ins i've watched the neuron tracing 1.0 and 2.0 videos but both seems to require that either you landmark the begining and end of you neuron or paint it which is obviously where is my difficulty: it is very hard the visually detect it so i'd like to make it automatic (especially in cross XY-Z directions)
Oct 7, 2016 04:10 PM | Manuel FOSSA - M2C
RE: Color tracing
Hello Hanchuan,
Yes the best thing to do is to show you my data. In attached file you have a subset of my data.
Remember that X and Y are spacial axis (longitude and latitude) and Z is time. As you can see you have some kind of fibers with high intensity areas. If you look along the Z axis you can see that on the right of the volume there are some high intensity areas that seem to be connected (there are gaps in between them but it is obvious they are actually the same pattern from time T0 that evolves in the X and Y dimensions during time (along Z)).
What i'd like to do is to automatically connect those points so as to show the line that the high intensity point à T0 followed.
Of course here you can draw a 3D line because the line is easily identified visually, but some other may not be that easy.
Is it possible to do something like that with Vaa3D?
Thanks!
Yes the best thing to do is to show you my data. In attached file you have a subset of my data.
Remember that X and Y are spacial axis (longitude and latitude) and Z is time. As you can see you have some kind of fibers with high intensity areas. If you look along the Z axis you can see that on the right of the volume there are some high intensity areas that seem to be connected (there are gaps in between them but it is obvious they are actually the same pattern from time T0 that evolves in the X and Y dimensions during time (along Z)).
What i'd like to do is to automatically connect those points so as to show the line that the high intensity point à T0 followed.
Of course here you can draw a 3D line because the line is easily identified visually, but some other may not be that easy.
Is it possible to do something like that with Vaa3D?
Thanks!
Nov 6, 2016 03:11 AM | Hanbo Chen - the university of georgia
RE: Color tracing
Color separator will extract a gray scale image of a connected
component to the seed region that (1) have similar colors and (2)
spatially connected. If there is a small gap, you can enlarge the
window size to jump the gap. But if the gap is too large, the
program may not be working well.
To use the plugin:
1: load image and open 3D view.
2: define a marker by right click on the neuron you want to trace and select to create a marker in the drop down menu.
3: launch neuron_color_separator in the plugin menu and it will pop up a window for you to set parameters and extract.
Hope it will work for you.
To use the plugin:
1: load image and open 3D view.
2: define a marker by right click on the neuron you want to trace and select to create a marker in the drop down menu.
3: launch neuron_color_separator in the plugin menu and it will pop up a window for you to set parameters and extract.
Hope it will work for you.