Read a File with coordinate XYZ in ImageJ

Usage & Issues
#1

hello everyone,

one question about his program: is it possible to read a File with x y z (fract. coordinates? or this program only read imagen?

Now, I try to explain me. I am studying a one type of defects. The material is silicon. I would want to compare three situation: the imagen HRTEM proposed in an article; the imagen by JEM-2100 (microscope to my laboratories); and the defect structure. For that,I generate a defect structure with dynamic molecular (lammps). Then, I extract the lattice with a defect that I want to study. Now, I would like to get its imagen HRTEM. Is it possible with this program? I know that here are other program to generate the Imagen HRTEM for this lattice, but my supervisor told me that this software is better that otrher program. However, I read the manual and I don’t know how to do it.by ImageJ

I know that his program is used to improve the quality of the HRTEM image, but I have not seen the function to read XYZ coordinates. Do You know it?

Thaks you for your attetions

#2

Welcome to the forum, @mruizprieto17!

Did you try the File :arrow_forward: Import :arrow_forward: Text Image… command? This opens a text image.

If it does not work, post one of your files here and we can offer more suggestions.

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#3

Thanks for you attentions,

I try this command and I don’t see the image. My Files called coordinateXYZ.txt is the type with list of coordinate XYZ, the document have three columns where each column is a coordinate component. For exaples:

10.43342 30.568 1.001
32.4083 22.761 1.012
10.41954 26.654 1.016
20.0912 36.375 1.018
32.3306 30.438 1.028
21.4751 38.301 1.029
10.47002 34.489 1.031
15.9464 18.793 1.04
31.0311 24.671 1.04
30.989 28.501 1.044
25.5555 36.323 1.046
14.6299 36.43 1.053
15.9993 38.367 1.054
10.44809 22.725 1.066
14.583 20.729 1.07
26.9514 38.246 1.075
30.9727 32.372 1.082
9.12017 32.545 1.084
25.6818 16.864 1.087
9.10437 28.608 1.09
32.3973 26.599 1.099
9.10967 24.683 1.118
20.1526 16.82 1.123
20.2054 40.294 1.129
32.3787 34.279 1.14
31.1706 20.75 1.143
9.17588 36.468 1.143
…

It is possible that this format may not read.

#4

Hi @mruizprieto17,

this file with XYZ coordinates is no image, right? Am I also right, if I think that this file results from some kind of image processing? The microsocope delivers something like a TIF image and some other program generates the list of coordinates from it?
It would surely be possible to read the data from that text file in, and to process it further. But to guide you in the right direction, it would be useful for us, if you could explain us a bit what kind of information is stored in that file… And what do you want to do with this information?

Cheers,
Robert

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#5

Yes haesleinhuepf, I try to explain my aim.

I have three option two compare the structure a analyse. First, I have

1280×720 86 KB
1280×720 167 KB
a Image HRTEM by one article (imagen1). Second, I have a Image obtained by microscope JEM-2100 (this image isnot attached). Third, I have the File with coordinate XYZ. This file contains the structure of defects. I would like to get the TEM image of this structure. For example, there is a software called QSTEM (http://qstem.org/ that permit to reproduce a Image TEM for this structure (image2).

My supervisor of PhD told me that ImageJ is better that QSTEM to generate the the image TEM from this structure. I don’t know that it is possible. I know this sotfware It is used to improve the image obtained from the telescope.

Then, I try to generate my image TEM from coordinate XYZ of structure of defects by ImageJ. But, First, I need to read the coordinate, don`t I? or Asre you see another way to compare the estruscturas of defet and the image on this article ?

thanks for your help

Manuel

#6

Hi Manuel,

I’m afraid that there is no ready-to-use plugin in ImageJ which allows you to do your analysis. According to this website:

https://groups.google.com/forum/#!topic/qstem/9G9VxiBp0xg

you may need to do some programming on your own. Professor Koch (QStem author) says “3. I recommend to do any quantitative processing of images in either DM, Matlab, Python, or ImageJ. Functiosn for importing those images into DM and Matlab are provided, and you are welcome to write more import functions. The data format specifications are on the website.”

But why not asking him, if/where there is any tool availabe which may support your work?

Cheers,
Robert

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#7

Thanks you for help me.

I will try to speak with Profesor Koch. Him software have more option to configgure the Image. And them, It is possible to combine QSTEM with imageJ. First, I will speak with them

Thanks youuuu :slight_smile: .

#8

Hi Manuel,

I am having the same question as you posted here. Did you find out how to read xyz file in ImageJ? Or maybe an approach to convert from xyz file to readable format in ImageJ? Can you please share your experience?

Thank you very much!

#9

Hi vutruong,

I can`t know if ImageJ is possible to read a file with xyz and then it simulated the imagen HRTEM. I solved the problem with two ways.

My research inmicroscopy has two parts:
1º- I study evolution of defects with LAMMPS. Then, I have a file with XZY coordinates. Later, I use QSTEM to reproduce the image HRTEM and compare with experimental images…You download QSTEM in http://qstem.org/. This part is by computer. Then, you can improve the image with imageJ
2º I generate a sample of silicon with defects by ion implant. Then, I explore and acquire the imagen experimental in laboratory by microscopy. That image was improved by ImageJ. Finally, I try to compare the imagen simulated by LAMMPS/QSTEM with the image experimental.

But, Why do you want to read xyz file? Do I answer your question?

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#10

Hi,
I’m sorry just read your message now. I’m doing a simulation of water slabs and just trying to use ImageJ to analyze my data. There is nothing related to experiment in my project. I got your point anw. Thank you very much!

Vu T.

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