caMicroscope
Replies: 38 comments 97 replies
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Hello @SisiVero You are not required to clone all the 30 repos to your local machine, you are to clone the Distro repo. |
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Okay noted thanks |
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Thanks gbenga this reaaly helped |
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glad it helped. |
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Hello @PASEDA-MODUPE , were you able to install docker? |
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@SisiVero yes I was, any issue on your side?? |
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In the project communication information area there was a part were it is required by applicants to take a tutorial before before making contributions, if so how do we proceed with that. |
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Hello @We13b-MD, I think @birm pointed our attention to the caMicroscope documentation, you will get most of the guidelines there. |
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Ok |
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@We13b-MD I started by downloading the docker desktop .exe file, use this link https://docs.docker.com/desktop/install/windows-install/ for guidance. Please reach out if any issue encountered in the process :) |
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@NgweBecky please I have troubles getting started |
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I am facing this when trying to upload the image, could anyone possibly see my mistake? |
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I initially noticed it while I was reading, but when I went back to look for it, I couldn't find it again. Do you happen to have any insights that could help me with this? I would greatly appreciate your assistance |
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Let's try to convert the image file to either Digital Imaging and Communications in Medicine (DICOM) format or proprietary formats like Aperio (.svs) or Hamamatsu (.ndpi). Let's see how this goes. |
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That works, thanks
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@gbengaoluwadahunsi Is that how the response should look like? |
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The first column is showing an error -3001 |
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I'm going to drop this link here; http://camicroscope.org/docs/ I'm going to be a little slow getting to all of the responses; so many interested people! |
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Thanks @birm, this will be helpful |
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Thank you @birm |
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Thank you |
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This is actually really helpful. Thank you |
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Thanks @birm |
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@gbengaoluwadahunsi please can you help with a valid medical image. I keep getting errors |
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@gbengaoluwadahunsi , this link is showing not found on my end, is there anything you did to access it? thanks for your response |
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Hello @We13b-MD , I faced the same issue. Do let me know as it goes and if you need further assistant. |
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ok thank you |
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@SisiVero did the bios setup it worked thanks alot |
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@We13b-MD ,yourw welcome |
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@birm @nanli-emory please any sugeestion on why I get a -3001 error when I upload a DICOM image. |
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I think we need to install a dependency to fix ca-load or else we won't overcome that, with Mac users, that is easier to fix, I am trying now to figure out how to make ca-load work on my Windows, I might be migrating my development to the Mac/Ubuntu ecosystem henceforth, laughs. |
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It is tough figure that out for me since the docs does not make mention. Thanks, I will have a look too |
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Yes, that would be one of the suggestions we are going to make to the caMicroscope docs, the backend should be run through so that users shortly don't face the same glitch. |
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I'm experiencing the same issue that @NgweBecky described. Has anybody been able to overcome this? |
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I think this may be related to this issue -- https://github.com/orgs/camicroscope/discussions/668 |
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has anybody been able to upload ? i will appreciate some help |
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@gbengaoluwadahunsi it shows not found for me, please help |
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@NgweBecky , click the link again |
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works now, thanks |
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@NgweBecky , you are welcome |
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@gbengaoluwadahunsi , THANK YOU so much ...though after uploading, its still showing not compatible |
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did you download the svs image type pls?
…On Thu, Mar 7, 2024 at 9:53 PM Khadijaarike ***@***.***> wrote:
@gbengaoluwadahunsi <https://github.com/gbengaoluwadahunsi> , THANK YOU
so much ...though after uploading, its still showing not compatible
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yes i did downloaded the svs |
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@Khadijaarike , you ought to fill in the Filename with CMU-1.svs and the slidename input name too. |
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Thank you very much will check it out
…On Thu, Mar 7, 2024, 5:50 PM SisiVero ***@***.***> wrote:
Hello @We13b-MD <https://github.com/We13b-MD> , I faced the same issue.
First of you need to know the BIOS key of your laptop. How do you know
that? By searching "Your laptop model BIOS key". Once you get the answer,
restart your laptop and continue pressing the key, it will bring out the
settings. Go to CPU configuration, scroll down to virtualization or virtual
machine, and enable it.
If you make use of HP Pavilion, I shared how I was able to solve mine
here:
#690 (comment)
Do let me know as it goes and if you need further assistant.
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Has anyone been able to successfully upload an image? It appears a lot of us are having a hard time doing that. |
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I need assistance with docker. So i have successfully installed it and also cloned the distro repo. I am stuck at running caMicroscope locally. I was going through the docker documentation and the project folder is supposed to have a Dockerfile but i am not able to locate it. |
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@DIANAAJAMBO , fork and clone this https://github.com/camicroscope/caMicroscope and have a good time contributing. |
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Okay. Since it's experimented and worked fine. |
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I faced the same challenge while setting up the project. It seemed the session was running for too long. But I noticed that I didn't have to wait for it to run to completion to see the landing page. So, @DIANAAJAMBO, when you try to run it again, check the "port" column in the docker app (I've added a screenshot). If the 4010:4010 port appears, click it. That's the landing page. You'll notice in the screenshot that not all the containers are running. So in the command prompt, it will still appear to be running without end. Try this and let us know how it goes.
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@nwanduka Thank you so much. I looked for that port and it was able to access the landing page. @gbengaoluwadahunsi and @SisiVero, yes my docker was able to build and run very fast. I also just noticed i needed to find the 4010 port like @nwanduka has showed me. Thanks to you all. |
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Awesome. I'm glad we figured that out. |
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@gbengaoluwadahunsi please guide me on how to run the project locally if it there is a way. I have tried doing so using node and npm but it is not working, am I missing something? |
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You can't run with just npm. I'd start with the instructions at https://github.com/camicroscope/distro |
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Thank you @birm , I guess she is talking bout the caMicroscope viewer repo, @NgweBecky , just just have to locate the index.html file in the cloned repo and open it , it will pop up in your browser, you can then proceed with the various html, css and JS files you want to work with. |
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thank you @ and @birm, I did that earlier and thought I missed it. thanks again |
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Hii, once we make changes in the UI using camicroscope repo, how can we view those changes on the site? |
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I also had this issue I suggest get the rocker engine running first then you go to the terminal and write the command docker-compose -f caMicroscope.yml up |
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recommended to run first the
|
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And you need to have a solid internet connection |
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@gbengaoluwadahunsi @SisiVero @birm when building i got this error: OSError: libopenslide.so.0: cannot open shared object file: No such file or directory how do i solve this |
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I think this is related to https://github.com/orgs/camicroscope/discussions/668. Can you provide some more logs, and tell us what system you're using? |
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@ birm I am using WSL for windows ubuntu: |
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@birm , I was able to load the image file but after the completion, it kept showing -3001 and the terminal shows it's partly becos of the ca-load not connecting. some of us too are facing similar glitches as mine, what should I do. |
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@SanjanaSogimatt and @gbengaoluwadahunsi please where you able to run caracal repo locally? Please could you put me through how you were able to successfully run the project locally |
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Let me try and open my github account
…On Thu, Mar 14, 2024, 12:23 AM Moliki-Salman Damilola Aminah < ***@***.***> wrote:
@SanjanaSogimatt <https://github.com/SanjanaSogimatt> and
@gbengaoluwadahunsi <https://github.com/gbengaoluwadahunsi> please where
you able to run caracal repo locally? Please could you put me through how
you were able to successfully run the project locally
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Here is the link to a simplified guidehttps://
github.com/orgs/camicroscope/discussions/712#discussioncomment-8727836
I am not with my PC, that is the reason it took me so long.
…On Thu, Mar 14, 2024, 1:59 AM Victoria Nduka ***@***.***> wrote:
Here you go @SanjanaSogimatt <https://github.com/SanjanaSogimatt>
Contributing Guide: https://camicroscope.org/contributing.html
Contributor Tasks:
https://github.com/camicroscope/GSOC/blob/master/ContributorTasks.md
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@gbengaoluwadahunsi , Thank you for your prompt response. However, I have done all what you described in your previous post. I have already created a discussion on the exact problem i am experiencing in a separate channel , so I will drop it here. PLEASE KINDLY GUIDE ME. I am trying to setup the caracal repository locally and run it. I have cloned all the three required repository (caracal, Distro and caMicroscope) in a parent directory as instructed in the caracal readme.md. However, I am unable to run bash ./setup_script inside the caracal repo. whenever i try to run it, it throws " [ database ] : name not passed, set to default value (127.0.0.1) Also, i want to clarify. The readme.md of caracal repo states that: "First clone the [Caracal (backup-dev branch)], but I could not see a branch named backup-dev branch under Caracal. I only cloned Caracal. I look forward to your guidance. Thank you |
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Even I am getting the same thing |
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@Moliki-Salman did you figure out how to do it? |
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Oh, I quite understand your point,
Unfortunately, I am facing the same problem as regards running the three
repositories on one server locally.
I think we should call on @birm to put us through.
Thanks
…On Thu, Mar 14, 2024, 2:39 AM Moliki-Salman Damilola Aminah < ***@***.***> wrote:
@gbengaoluwadahunsi <https://github.com/gbengaoluwadahunsi> , Thank you
for your prompt response. However, I have done all what you described in
your previous post. I have already created a discussion on the exact
problem i am experiencing in a separate channel , so I will drop it here.
PLEASE KINDLY GUIDE ME.
I am trying to setup the caracal repository locally and run it. I have
cloned all the three required repository (caracal, Distro and caMicroscope)
in a parent directory as instructed in the caracal readme.md. However, I am
unable to run bash ./setup_script inside the caracal repo. whenever i try
to run it, it throws " [ database ] : name not passed, set to default value
(127.0.0.1)
[ database ] : name not passed, set to default value (camic)
mongo could not be found on path. Please ensure that mongo is installed
and is on PATH". I have installed mongo but i am still unable to run the
script.
Please kindly guide me on what to do to solve this problem.
Also, i want to clarify. The readme.md of caracal repo states that: "First
clone the [Caracal (backup-dev branch)], but I could not see a branch named
backup-dev branch under Caracal. I only cloned Caracal.
I look forward to your guidance. Thank you
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I will try it one more time and let you know.
…On Thu, Mar 14, 2024, 2:13 PM Sanjana ***@***.***> wrote:
Thanks, @nwanduka <https://github.com/nwanduka>
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Guys, can anyone see the loading page being rendered while navigating through other segments in the page? Because I can't |
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For which repo?
Distro or caMicroscope
…On Thu, Mar 14, 2024, 2:31 PM Sanjana ***@***.***> wrote:
Guys, can anyone see the loading page being rendered while navigating
through other segments in the page? Because I can't
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caMicroscope |
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Ya so when you try to navigate, it shows a blank white screen rather then the loading animation |
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Nope, it works perffectly |
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Okay, cool |
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alright. |
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Here #686 (comment)
…On Thu, Mar 14, 2024, 6:29 PM sangwan-smriti ***@***.***> wrote:
what to do after uploading slide? where are tasks list given for the
project?
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@gbengaoluwadahunsi , @SanjanaSogimatt , Does this you have not been able to make a contributions on the project too? Because I have not been able to move a step further ever since I am unable to run the repos. Please kindly clarify because I feel hanged OR are there other ways we can contribute pending the time that @birm would be able to guide us on how to fix the problem |
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Yup same here, I am on this for the whole day but still can't figure out. But we can contribute to other repos |
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If you want to make contributions to the frontend development of the
project, you can kindly clone the caMicroscope repo and effect your changes
there and make a PR.
…On Fri, Mar 15, 2024, 12:11 AM Moliki-Salman Damilola Aminah < ***@***.***> wrote:
@gbengaoluwadahunsi <https://github.com/gbengaoluwadahunsi> ,
@SanjanaSogimatt <https://github.com/SanjanaSogimatt> , Does this you
have not been able to make a contributions on the project too? Because I
have not been able to move a step further ever since I am unable to run the
repos. Please kindly clarify because I feel hanged OR are there other ways
we can contribute pending the time that @birm <https://github.com/birm>
would be able to guide us on how to fix the problem
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Hi all, I currently have a project running locally. Can someone or one of the maintainers guide me on what to do next? Apologies if I am missing anything. |
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I hope it's clear now?
If you can't figure it out the Distro frontend end, move to the
caMicroscope.
…On Fri, Mar 15, 2024, 12:51 AM Sanjana ***@***.***> wrote:
Yup same here, I am on this for the whole day but still can't figure out.
But we can contribute to other repos
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Hi, which of the repo do you have running locally?
If it's the Distro, you have to try to upload a slide image and play around
with the view.
If it's the caMicroscope, you have to check the contribution ReadMe file
and try to fix the issue in the list or suggest a feature on the frontend
of the project.
If it's the carcal repo, it's the backend codes for the project, check the
contribution ReadMe file and try to implement your contributions.
You can then push your contributions to the caMicroscope project by making
a PR.
I hope this helps.
…On Fri, Mar 15, 2024, 1:00 AM Sanket Pol ***@***.***> wrote:
Hi all, I currently have a project running locally. Can someone or one of
the maintainers guide me on what to do next? Apologies if I am missing
anything.
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Disto. Now I got it |
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Hello @birm , having read the intern task, So, if I understand well, I am required to clone the repos for this project, then run it and see how it works. Then suggest changes to ui if any and then try and make it a standalone executable, yes? I have few other questions regarding the draft you shared.
If understand correctly, I am to clone the repositories , the 30 of them? Then install the Docker and Docker compose and run caMicriscope locally to experiment it, yes?
Now, when you said to add a Slide to my instance of caMicriscope, what do you mean?
I'm sorry I'm asking lots of questions. I just need to be sure I'm on the right path.
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