Pre-trained model weights - official release, version 1.2

[rossbar]

Pre-trained model weights have been officially released and are now available via the deepcell access portal at https://users.deepcell.org. The first official release of models/datasets are version 1.2.

Model access

Pre-trained models and training datasets are licensed under a modified Apache license for non-commercial academic use only. Account requests to https://users.deepcell.org/ are automatically evaluated for license compliance. In some cases, particularly for non-.org and .edu domains, manual review is required, which can take several days.

Quickstart

Users can ensure they have access to the latest weights by:

1. Updating the codebase; i.e. git pull and reinstall or follow the installation instructions
2. Set your deepcell access token: e.g. export DEEPCELL_ACCESS_TOKEN=<token-generated-on-users.deepcell.org>
3. Downloading the latest pre-trained model weights: python -c "import cellSAM; cellSAM.get_model();"
4. (Optional) downloading the evaluation dataset: python -c "import cellSAM; cellSAM.download_training_data();". The dataset is not required for inference, but is provided for reproducibility.

See the documentation for more information.

Previous pre-trained weights

There have been previous model weights released to aid in review/preliminary evaluation of the work. These are no longer compatible with the latest software release and have been superseded by the v1.2 release.

• cellsam_base.pt
• cellsam_base_v1.1.pt

Reproducibility

The official weights can be used to reproduce the results in the publication. See the docs on reproducibility for details.

[mario-koddenbrock]

Hi!

I’m trying to register via the DeepCell portal (for access to the new pre-trained models), but I never receive any confirmation or activation email. I’ve tried with several different email addresses and still nothing comes through. Could you please check whether the registration emails are being sent (or blocked), or provide an alternate way to gain access?

Thanks!

[mario-koddenbrock]

Hi!

I’m trying to register via the DeepCell portal (for access to the new pre-trained models), but I never receive any confirmation or activation email. I’ve tried with several different email addresses and still nothing comes through. Could you please check whether the registration emails are being sent (or blocked), or provide an alternate way to gain access?

Thanks!

solved! thanks!

[amthreeh]

Hi!
I’m trying to register via the DeepCell portal (for access to the new pre-trained models), but I never receive any confirmation or activation email. I’ve tried with several different email addresses and still nothing comes through. Could you please check whether the registration emails are being sent (or blocked), or provide an alternate way to gain access?
Thanks!

solved! thanks!

How to solve it? I can't log in Deepcell portal.

[mario-koddenbrock]

So, after writing this issue, it seems like someone unlocked my registration. By the way, writing the contact forms didn’t seem to help.

[eezaynah]

I have the same problem as described above. How can I solve it?

[eezaynah]

• cellsam_base_v1.1.pt

I have the same problem as described above. How can I solve it?
Your username and password didn't match. Please try again.

Deepcell Users
Note

Once your account is successfully created, your username is your registration email without the domain suffix. For example, if your registration email is foobar@baz.edu, your Deepcell username is `foobar

I can't log in.

[trushbin]

Hi, I'm facing this problem as well. I used my university email to sign up for an API Key, but I can't log in. I hope there's a fix for this. Thanks.

[apanagar]

I'm having the same issue. Is this system automated or is there someone manually approving accounts? Also the lassword reset doesn't send any email.

[macromeer]

Same issue.

[rossbar]

I'm having the same issue. Is this system automated or is there someone manually approving accounts? Also the lassword reset doesn't send any email.

There is an automated system in place; however, it does not reliably handle all non-profit domains, so many requests do require manual approval which can take several days. We apologize for the inconvenience of having to wait for this approval.

[rossbar]

For those having issues with users.deepcell.org accounts - I've updated the OP with info about account registration approval - for non-.edu domains it can take several days depending on whether the requesting domain is already recognized as a non-profit institution.

[apanagar]

For those having issues with users.deepcell.org accounts - I've updated the OP with info about account registration approval - for non-.edu domains it can take several days depending on whether the requesting domain is already recognized as a non-profit institution.

I'm not academically affiliated, I am just exploring some of the modern cell biology vision models for personal interest. Is registering with a gmail account and without an institution troublesome?