Welcome to TopoStats Discussions! #39
Replies: 14 comments 30 replies
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Hi everyone, Thank you to all those who have worked on this software. I'm conducting a summer research project involving AFM imaging and DNA measurements. My project has a lot of images involved and many DNA fragments so an automated measurement software would be fantastic. I'm very new to python and was wondering if there was an installation guide or tutorial for implementing TopoStats for use in my project? Thanks again. |
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Hi @jrobert21! There's some stuff here #10 not sure if it's 100% reliable. I belive a proper install guide is on its way. @Jean-Du may be able to say more. There's also a potential way forward with docker (if you're into that sort of thing) #44. |
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Hi here is an installation guide for using TopoStats with PyCharm in Windows |
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Hello! My name is Ankush Dhawan, and I am a researcher in the Mai Group at Stanford University working on imaging DNA in confinement. I came across your work when working on image processing. I wanted to test out Topostats, as it looked super promising for helping me achieve my goals. Is there a guide/readme file that explains how I can begin using Topostats on my computer with my own images (I have access to both a MacBook and a Windows computer, and can use whichever is the most compatible)? Thank you, |
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Hi, we have a guide on how to install TopoStats on windows: The file to start working with is pygwytracing.py, and we have a guide explaining how it works here: If you haven't already, please do also check our publication, which gives a detailed explanation on what TopoStats does |
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Try chaging Line 13 in 4ad2ab1 - wincertstore==0.2 in your downloaded gwyconda.yml (removing the version constraint). Please let me know if this helps :)
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Try getting rid of the |
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Thanks for getting in touch again @aswinkl24 - I'm having a think! |
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Can you please enter |
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32-bit Python 2 is definitely required. Is it available here? https://repo.anaconda.com/archive/Anaconda3-2021.05-Windows-x86.exe |
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Will Anaconda3 allow a python 2 environment? |
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Have you tried the new Docker install? |
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Do let me know how you get on. Sorry I've not been more responsive on this thread. |
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Hello everyone, thank you to all the members of the team who have worked on this software. I have installed the software TopoStats and tried to analyze the AFM imaging with help of it. The AFM imaging was converted from the ibw format into the spm format. The software has found the image but it has the problem with the analysis. My output was 0%. What should I do to analyze my imaging successfully? Thank you. Best regard |
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Hello @mary82104 ! Thank you for using our software, it means a lot to us. Could you share the output that is given when you try to run TopoStats by copying it and pasting it in a text file and uploading it here? It would greatly help in us assisting you 👍 (the entire output would be great - from when you typed the command to when it stops) In the meantime, does the output stop once it says 0%? Usually when running TopoStats, I find that it can pause multiple times for a few seconds when processing images. |
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Hello Sylvia. Thank you for your answer. Ich have tried today once more this image to analyze with the help of the software. It was the result.
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Thank you for sharing the log. It seems that the folder that TopoStats is looking in ( If you wanted it to search for .spm files there, then please could you check to see if that folder has your .spm files inside it? It seems like you might have wanted TopoStats to look inside Here is how to make a config file: In order to make a config file and tell TopoStats where to look for files, please copy this text, make a file called Then to run TopoStats using this configuration: where you should replace For example if you put I hope this helps, but do say if it doesn't. |
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Hello Sylvia Whittle,
thank you for your help. I have made a file" my_config.yaml" and placed it
into D:\test\Data\my_config.yaml\spm.spm ." Spm.spm "is the file with the
image that I want to analyze. It was the result.
[image: test1.png]
Am Fr., 25. Nov. 2022 um 17:58 Uhr schrieb Sylvia Whittle <
***@***.***>:
… @mary82104 <https://github.com/mary82104>
Thank you for sharing the log. It seems that the folder that TopoStats is
looking in (C:\Users\pharma) does not have your .spm files inside it. Did
you mean for the software to search C:\Users\pharma for your .spm files,
or did you want it to search elsewhere?
If you wanted it to search for .spm files there, then please could you
check to see if that folder has your .spm files inside it?
It seems like you might have wanted TopoStats to look inside C:\test\Test\
for your .spm file. If this is the case then you can tell TopoStats to look
there by editing a config file.
Here is how to make a config file:
base_dir: ./tests/
output_dir: ./output
warnings: ignore
cores: 4
quiet: false
file_ext: .spm
loading:
channel: Height
filter:
run: true # Options : true, false
threshold_method: std_dev # Options : std_dev (default), otsu, absolute
otsu_threshold_multiplier: 1.0
threshold_std_dev:
lower: 10.0
upper: 1.0
threshold_absolute:
lower: -1.0
upper: 1.0
gaussian_size: 1.0121397464510862 # in px
gaussian_mode: nearest
grains:
run: true # Options : true, false
# Thresholding by height
threshold_method: std_dev # Options : std_dev, otsu, absolute
otsu_threshold_multiplier: 1.0
threshold_std_dev:
lower: 10.0
upper: 1.0
threshold_absolute:
lower: -1.0
upper: 1.0
direction: upper # Options: upper, lower, both (defines whether to look for grains above or below thresholds or both)
# Thresholding by area
absolute_smallest_grain_size: 100
absolute_area_threshold:
upper: [ 400,600 ] # above surface [Low, High] in nm^2 (also takes null)
lower: [ null, null ] # below surface [Low, High] in nm^2 (also takes null)
grainstats:
run: true # Options : true, false
cropped_size: 40.0 # Length (in nm) of square cropped images (can take -1 for grain-sized box)
save_cropped_grains: true # Options : true, false
dnatracing:
run: true # Options : true, false
plotting:
run: true # Options : true, false
save_format: png # Options : see https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
image_set: all # Options : all, core
zrange: [null, null] # low and high height range for core images (can take [null, null])
colorbar: true # Options : true, false
axes: true # Options : true, false (due to off being a bool when parsed)
cmap: nanoscope # Options : nanoscope, afmhot
histogram_log_axis: false # Options : true, false
In order to tell TopoStats where to look for files, please copy this text,
make a file called my_config.yaml, paste this text inside it. Then place
the file in C:\test\Test\ or wherever you would like to keep it. The
first line of the file is where you tell TopoStats where to look for files.
In your case, you might want to change it to: base_dir: C:\Users\pharma\.
Save and close the file.
Then to run TopoStats using this configuration:
run_topostats --config "path_to_your_config_file"
where you should replace path_to_your_config_file with the path to where
you saved your config file. (This is just to tell it where to look for the
config file).
For example if you put my_config.yaml inside C:\Users\pharma\ then run: run_topostats
--config "C:\Users\pharma\".
I hope this helps, but do say if it doesn't.
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Hi @mary82104 Apologies for the delay. I meant that you should place the file inside the folder with your data, for example the folder containing your data might look like this: D:\test\Data:
Then you should be able to run: If you're still stuck, perhaps try reading through the documentation that we have written on how to get set up: https://github.com/AFM-SPM/TopoStats/blob/main/docs/usage.md But do tell me if you get stuck with it! 😄 |
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Hi Sylvia Whittle,
thank you for your answer. I have put the file 'my_config.yaml' into the
folder with my data. The TopoStats has created the output and put it into
Test/my_config.yaml/Processed/spm/filters/grains. But the both folders
(filters and grains) are empty. The Topostats has found and analyzed
together with our image the images from the file'minicircle' from the
folder' tests' from Topostats. The software has created the output with a
lot of pictures. I think it means that we should change some parameters of
our image in order to analyze it with your programm. Our image has pores.
It is the image of the peptidoglycan sacculus. I can send you our image if
you have time to have a look at it. You have maybe some ideas what
parameters we should change.
Once more thank you for your help.
Best regard
Maryna
Sylvia Whittle ***@***.***> schrieb am Di., 6. Dez. 2022,
17:10:
… Hi @mary82104 <https://github.com/mary82104>
Apologies for the delay. I meant that you should place the file inside the
folder with your data, for example the folder containing your data might
look like this:
|----- D:\test\Data ------|
| |
| - my_config.yaml |
| - spm.spm |
Then you should be able to run: run_topostats --config my_config.yaml in
the terminal from there.
If you're still stuck, perhaps try reading through the documentation that
we have written on how to get set up:
https://github.com/AFM-SPM/TopoStats/blob/main/docs/usage.md
But do tell me if you get stuck with it! 😄
—
Reply to this email directly, view it on GitHub
<#39 (reply in thread)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/A4L2A765XQGSBDDP2FC5CQDWL5QORANCNFSM4XUJQRXA>
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Thank you for your persevering with this! |
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Hello Sylvia Whittle,
apologies for the delay. I am very thankful, that you help me. This is the
spm file . I hope you can open it. But do tell me please if it cannot be
opened.
Once more thank you very much for your help.
Best regard
Maryna
Marina Warkentin ***@***.***> schrieb am Do., 1. Dez. 2022,
12:30:
… Hello Sylvia Whittle,
thank you for your help. I have made a file" my_config.yaml" and placed it
into D:\test\Data\my_config.yaml\spm.spm ." Spm.spm "is the file with the
image that I want to analyze. It was the result.
[image: test1.png]
Am Fr., 25. Nov. 2022 um 17:58 Uhr schrieb Sylvia Whittle <
***@***.***>:
> @mary82104 <https://github.com/mary82104>
>
> Thank you for sharing the log. It seems that the folder that TopoStats is
> looking in (C:\Users\pharma) does not have your .spm files inside it.
> Did you mean for the software to search C:\Users\pharma for your .spm
> files, or did you want it to search elsewhere?
>
> If you wanted it to search for .spm files there, then please could you
> check to see if that folder has your .spm files inside it?
>
> It seems like you might have wanted TopoStats to look inside
> C:\test\Test\ for your .spm file. If this is the case then you can tell
> TopoStats to look there by editing a config file.
>
> Here is how to make a config file:
>
> base_dir: ./tests/
> output_dir: ./output
> warnings: ignore
> cores: 4
> quiet: false
> file_ext: .spm
> loading:
> channel: Height
> filter:
> run: true # Options : true, false
> threshold_method: std_dev # Options : std_dev (default), otsu, absolute
> otsu_threshold_multiplier: 1.0
> threshold_std_dev:
> lower: 10.0
> upper: 1.0
> threshold_absolute:
> lower: -1.0
> upper: 1.0
> gaussian_size: 1.0121397464510862 # in px
> gaussian_mode: nearest
> grains:
> run: true # Options : true, false
> # Thresholding by height
> threshold_method: std_dev # Options : std_dev, otsu, absolute
> otsu_threshold_multiplier: 1.0
> threshold_std_dev:
> lower: 10.0
> upper: 1.0
> threshold_absolute:
> lower: -1.0
> upper: 1.0
> direction: upper # Options: upper, lower, both (defines whether to look for grains above or below thresholds or both)
> # Thresholding by area
> absolute_smallest_grain_size: 100
> absolute_area_threshold:
> upper: [ 400,600 ] # above surface [Low, High] in nm^2 (also takes null)
> lower: [ null, null ] # below surface [Low, High] in nm^2 (also takes null)
> grainstats:
> run: true # Options : true, false
> cropped_size: 40.0 # Length (in nm) of square cropped images (can take -1 for grain-sized box)
> save_cropped_grains: true # Options : true, false
> dnatracing:
> run: true # Options : true, false
> plotting:
> run: true # Options : true, false
> save_format: png # Options : see https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
> image_set: all # Options : all, core
> zrange: [null, null] # low and high height range for core images (can take [null, null])
> colorbar: true # Options : true, false
> axes: true # Options : true, false (due to off being a bool when parsed)
> cmap: nanoscope # Options : nanoscope, afmhot
> histogram_log_axis: false # Options : true, false
>
> In order to tell TopoStats where to look for files, please copy this
> text, make a file called my_config.yaml, paste this text inside it. Then
> place the file in C:\test\Test\ or wherever you would like to keep it.
> The first line of the file is where you tell TopoStats where to look for
> files. In your case, you might want to change it to: base_dir:
> C:\Users\pharma\. Save and close the file.
>
> Then to run TopoStats using this configuration:
>
> run_topostats --config "path_to_your_config_file"
>
> where you should replace path_to_your_config_file with the path to where
> you saved your config file. (This is just to tell it where to look for the
> config file).
>
> For example if you put my_config.yaml inside C:\Users\pharma\ then run: run_topostats
> --config "C:\Users\pharma\".
>
> I hope this helps, but do say if it doesn't.
>
> —
> Reply to this email directly, view it on GitHub
> <#39 (reply in thread)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A4L2A7YSEACNZJY7SOWZKCTWKDV4ZANCNFSM4XUJQRXA>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
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Hi Sylvia,
there is one more file with our image.
Am So., 11. Dez. 2022 um 11:46 Uhr schrieb Marina Warkentin <
***@***.***>:
… Hello Sylvia Whittle,
apologies for the delay. I am very thankful, that you help me. This is the
spm file . I hope you can open it. But do tell me please if it cannot be
opened.
Once more thank you very much for your help.
Best regard
Maryna
Marina Warkentin ***@***.***> schrieb am Do., 1. Dez. 2022,
12:30:
> Hello Sylvia Whittle,
>
> thank you for your help. I have made a file" my_config.yaml" and placed
> it into D:\test\Data\my_config.yaml\spm.spm ." Spm.spm "is the file with
> the image that I want to analyze. It was the result.
>
> [image: test1.png]
>
> Am Fr., 25. Nov. 2022 um 17:58 Uhr schrieb Sylvia Whittle <
> ***@***.***>:
>
>> @mary82104 <https://github.com/mary82104>
>>
>> Thank you for sharing the log. It seems that the folder that TopoStats
>> is looking in (C:\Users\pharma) does not have your .spm files inside
>> it. Did you mean for the software to search C:\Users\pharma for your
>> .spm files, or did you want it to search elsewhere?
>>
>> If you wanted it to search for .spm files there, then please could you
>> check to see if that folder has your .spm files inside it?
>>
>> It seems like you might have wanted TopoStats to look inside
>> C:\test\Test\ for your .spm file. If this is the case then you can tell
>> TopoStats to look there by editing a config file.
>>
>> Here is how to make a config file:
>>
>> base_dir: ./tests/
>> output_dir: ./output
>> warnings: ignore
>> cores: 4
>> quiet: false
>> file_ext: .spm
>> loading:
>> channel: Height
>> filter:
>> run: true # Options : true, false
>> threshold_method: std_dev # Options : std_dev (default), otsu, absolute
>> otsu_threshold_multiplier: 1.0
>> threshold_std_dev:
>> lower: 10.0
>> upper: 1.0
>> threshold_absolute:
>> lower: -1.0
>> upper: 1.0
>> gaussian_size: 1.0121397464510862 # in px
>> gaussian_mode: nearest
>> grains:
>> run: true # Options : true, false
>> # Thresholding by height
>> threshold_method: std_dev # Options : std_dev, otsu, absolute
>> otsu_threshold_multiplier: 1.0
>> threshold_std_dev:
>> lower: 10.0
>> upper: 1.0
>> threshold_absolute:
>> lower: -1.0
>> upper: 1.0
>> direction: upper # Options: upper, lower, both (defines whether to look for grains above or below thresholds or both)
>> # Thresholding by area
>> absolute_smallest_grain_size: 100
>> absolute_area_threshold:
>> upper: [ 400,600 ] # above surface [Low, High] in nm^2 (also takes null)
>> lower: [ null, null ] # below surface [Low, High] in nm^2 (also takes null)
>> grainstats:
>> run: true # Options : true, false
>> cropped_size: 40.0 # Length (in nm) of square cropped images (can take -1 for grain-sized box)
>> save_cropped_grains: true # Options : true, false
>> dnatracing:
>> run: true # Options : true, false
>> plotting:
>> run: true # Options : true, false
>> save_format: png # Options : see https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
>> image_set: all # Options : all, core
>> zrange: [null, null] # low and high height range for core images (can take [null, null])
>> colorbar: true # Options : true, false
>> axes: true # Options : true, false (due to off being a bool when parsed)
>> cmap: nanoscope # Options : nanoscope, afmhot
>> histogram_log_axis: false # Options : true, false
>>
>> In order to tell TopoStats where to look for files, please copy this
>> text, make a file called my_config.yaml, paste this text inside it.
>> Then place the file in C:\test\Test\ or wherever you would like to keep
>> it. The first line of the file is where you tell TopoStats where to look
>> for files. In your case, you might want to change it to: base_dir:
>> C:\Users\pharma\. Save and close the file.
>>
>> Then to run TopoStats using this configuration:
>>
>> run_topostats --config "path_to_your_config_file"
>>
>> where you should replace path_to_your_config_file with the path to
>> where you saved your config file. (This is just to tell it where to look
>> for the config file).
>>
>> For example if you put my_config.yaml inside C:\Users\pharma\ then run: run_topostats
>> --config "C:\Users\pharma\".
>>
>> I hope this helps, but do say if it doesn't.
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#39 (reply in thread)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A4L2A7YSEACNZJY7SOWZKCTWKDV4ZANCNFSM4XUJQRXA>
>> .
>> You are receiving this because you were mentioned.Message ID:
>> ***@***.***>
>>
>
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Hi @mary82104 I'm sorry, I cannot see a file attached to your reply. I'm not sure why uploading a file doesn't work. Perhaps you could send the file along with your |
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Hi! As one of the great powers of this Python package is that it avoids the user bias associated with the initialization, I am very interested in using TopoStats to analyze some HS-AFM frames. I did not have any problems obtaining the preliminary statistics and processed image for the test dataset (total of 21 minicircles). I would ultimately like to obtain a height profile along the length of my biomolecule of interest (DNA bound to CTCF protein); thus, would you be willing to tell me how I can obtain the x, y, z values of the fitted trace into a .csv file? |
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Hi @connorcowie! Firstly, thanks for reaching out! Re: I would recommend trying it, we can help out if you are struggling! To install the development version of TopoStats, you can follow this guide :https://github.com/AFM-SPM/TopoStats/blob/main/docs/installation.md (Starting at the section "Cloning from GitHub"). Again, shout if you get stuck. Re: Re: Height profiles It's hard to say when we will have the time to add this, as the entirety of the tracing functions are being refactored and improved immensely at the moment, though I would strongly recommend giving it a go yourself with Python in the meantime. If I have some free time, I may give it a go too. Please do let me know if this hasn't answered your questions, or if you have follow-up questions. We really appreciate people using the software and giving feedback on how to improve it. |
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Hi @SylviaWhittle, |
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Hi @connorcowie, No worries on the delay. If it would help, I could write a small script to load Thank you for being understanding regarding the z-coordinates of the array. While it might be relatively trivial for us to do this, it would immediately have to be re-written as we are redoing our tracing scripts, and so we plan on doing it in the coming weeks as Regarding your installation troubles, I do not know why it would fail to install scikit-image. A brief look online does not come up with many suggestions. One thing to check is to make sure you create an anaconda environment with Python version 3.8+ (I'd recommend 3.10 personally as that is what I have been using). Another suggestion is to ensure that numpy is installed before scikit-image, so perhaps manually install numpy before trying to install topostats?: (commands from memory, might not be accurate) I will ask around the group to see if anyone has any ideas. |
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Correct- Those .TIFF files were obtained my processing the .ASD files in ImageJ. Your suggestions seemed to do the trick as far as avoiding the scikit-learn error message when trying to install the development version of TopoStats! However, my .ASD files within the topostats subfolder are still not being recognized and acted upon, bringing me back to the same issue as before (only searching for .SPM files). Is there an easy way to modify the search criterion or should the package be able to identify .ASD files automatically when there are no .SPM files in the subfolder? Thank you for bringing these issues to the attention of your other team members. |
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Yay!
Does that make sense? Please let me know if you have any issues, I might have got something wrong! Also have a play with the configuration options and please ask questions / suggest how we could improve our documentation on this. (signing off for now, will check back later) |
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Hi, D:\Program Files\python\Lib\site-packages\topostats>run_topostats I'm wondering if you could help me to solve this error. Thanks. Best wishes, |
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Hi @DakeMaoDNA , Thanks for getting in touch. I've started a new thread dedicated discussing this in the Q&A section, you can find it here. Please let us know if this solves your problem. Neil |
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Hello everyone, Thank you for your efforts on this software. I've encountered an error while trying to apply it to Gwyddion files. Despite changing the channel name to "Height" and the file type in my_config.yaml, I'm seeing the following error: "UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb5 in position 15: invalid start byte." I've attached a screenshot for reference. When testing it with Bruker .spm files in the same folder, no errors occurred. I'm unsure why this issue is specific to this Gwyddion files. Thank you, |
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Hi Sylvia, thank you so much for helping. Regarding the second image, indeed, the horizontal lines should not be there; probably something in the code caused it. The original image is 512*256, but I'm unsure if this is the problem causing the horizontal lines. Please let me know if you need anything else. |
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Thanks for clarifying. I haven't been able to find out why the data is stripy, but I will add the fix to enable loading of these files and then try to solve this stripy issue. May I use one of these images to add to our code for testing that our function works? Perfectly fine if you would rather that these images are not on our repo though! |
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Hi Sylvia, thank you so much for helping. Because the image we might use in future, probabaly I can send you few other similar images to add in code for test? Thank you! |
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Just a single image that you would be okay with being in our repo would be helpful so we can add it to our tests to make sure nothing breaks 😄 thank you. I am looking into the stripes issue too. |
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Test.zip |
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Greetings all, I am Vaishali Sharma, a 4th year PhD student at Michigan technological university, US. My work focuses on imaging viruses with AFM after antiviral treatments. I came across this after attending AFMBiomed school in 2022. Thank you all who have worked on this application to make the life a AFM user easy. |
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👋 Welcome!
We’re using Discussions as a place to connect with other members of our community. We hope that you:
build together 💪.
To get started, comment below with an introduction of yourself and tell us about what you do with this community.
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