where to set cellpose and stardist

[fabricesenger]

Hello Romain it's all in the title,
when i run imageJ in the biop/desktop the few features i tested are working nicely.
Next when i try the biop cellpose or stardist i have to specify where is the model , soooo, where are the default models located ?

Let me know if you need screenshots.

Besides that, QPath is starting up nicely ... I will continue testing

Fabrice.

[romainGuiet]

Hi @fabricesenger ,

I'm sorry I totally missed your post/message! I discovered it just now...

biop cellpose or stardist i have to specify where is the model

To enable the wrappers you need to :

• for Cellpose wrapper : specify where the environment is, using Plugin>BIOP>Cellpose setup... and specify /opt/conda/envs/cellpose/ . The default models are already installed, so you can use the plugin !

• for StarDist wrapper : specify where the environment is, using Plugin>BIOP>StarDIst3D setup... and specify /opt/conda/envs/stardist/ . You will need a StarDist3D model. As far as I know, there is NO official StarDist3D model, but we made one available on zenodo.

Best

Romain

[fabricesenger]

Hello Romain, don't worry. Thank you for your reply I will try it out ;) Any here and then I check the status of your project. If there's something I could try as beta-tester do not hesitate, Best, Fabrice. De: "romainGuiet" ***@***.***> À: "BIOP/BIOP-desktop" ***@***.***> Cc: "FABRICE SENGER" ***@***.***>, "Mention" ***@***.***> Envoyé: Mercredi 27 Mars 2024 14:59:49 Objet: Re: [BIOP/BIOP-desktop] where to set cellpose and stardist (Issue #4) Hi [ https://github.com/fabricesenger | @fabricesenger ] , I'm sorry I totally missed your post/message! I discovered it just now... biop cellpose or stardist i have to specify where is the model To enable the wrappers you need to : * for Cellpose wrapper : specify where the environment is, using Plugin>BIOP>Cellpose setup... and specify /opt/conda/envs/cellpose/ . The default models are already installed, so you can use the plugin ! * for StarDist wrapper : specify where the environment is, using Plugin>BIOP>StarDIst3D setup... and specify /opt/conda/envs/stardist/ . You will need a StarDist3D model. As far as I know, there is NO official StarDist3D model, but we made one available on [ https://zenodo.org/records/6645978 | zenodo ] . Best Romain — Reply to this email directly, [ #4 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXWLY5SDFPSFNTERZPXN2A3Y2K7ELAVCNFSM6AAAAABDKA7QSCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRSHA2DKNBYGM | unsubscribe ] . You are receiving this because you were mentioned. Message ID: ***@***.***>