Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Cell-detector installation failed #14

Open
hrch3n opened this issue Oct 7, 2021 · 6 comments
Open

Cell-detector installation failed #14

hrch3n opened this issue Oct 7, 2021 · 6 comments
Assignees
@jxchen01
Labels
WIP an issue being worked on

Comments

@hrch3n
Copy link

hrch3n commented Oct 7, 2021 •
edited
Loading

Description

The cell_detector.git couldn't be cloned. The error message is shown below:

git clone ssh://[email protected]:7999/assay/cell_detector.git
Cloning into 'cell_detector'...
ssh: Could not resolve hostname aicsbitbucket.corp.alleninstitute.org: Name or service not known
fatal: Could not read from remote repository.

Without cell detection, DNA_MEM_instance_plus_LF can't be run.
@jxchen01
Copy link
Collaborator

jxchen01 commented Oct 7, 2021

Thanks for your interest in our work. We are in the process of shipping the cell detector package from an internal bitbucket to this new public github organization.

Do you mind sharing what are you planning to do exactly? Testing on your own data? Or trying to reproduce our results? If possible, I would suggest to try our the basic version (the main difference is not using the bright field channel):

https://github.com/AllenCell/segmenter_model_zoo/blob/main/playbooks/demo_2_using_super_model.ipynb

Let me know if there is anything I can help at the moment, while we are working on the cell detector code shipping.

Thanks!
Jianxu

@jxchen01 jxchen01 added the WIP an issue being worked on label Oct 7, 2021
@jxchen01 jxchen01 self-assigned this Oct 7, 2021
@hrch3n
Copy link
Author

hrch3n commented Oct 7, 2021 via email

@jxchen01
Copy link
Collaborator

jxchen01 commented Oct 7, 2021

I see. In your specific scenario, you may have to re-train the models, since our models were pre-trained only on our 100x confocal microscopy images

@hrch3n
Copy link
Author

hrch3n commented Oct 7, 2021 via email

@jxchen01
Copy link
Collaborator

Thanks for the insights. I have to use pre-trained models due to the experiment design. The resolution for my image is 1x1x2 microns for each voxel. Which model in the zoo would you recommend for testing?
…
________________________________ From: Jianxu Chen @.> Sent: Thursday, October 7, 2021 3:24 PM To: AllenCell/segmenter_model_zoo @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [AllenCell/segmenter_model_zoo] Cell-detector installation failed (#14) I see. In your specific scenario, you may have to re-train the models, since our models were pre-trained only on our 100x confocal microscopy images — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD2AA2ZXNYC5JKXADVEWHA3UFXXV5ANCNFSM5FRPOTTQ.

I am afraid none of our pre-trained model will get good results off-the-shelf.

@hrch3n
Copy link
Author

hrch3n commented Jul 7, 2022 via email

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@jxchen01 jxchen01

Labels
WIP an issue being worked on
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@jxchen01 @hrch3n