How to apply pretrained model?

hrch3n commented 3 years ago

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (IMC) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

stegmaierj commented 3 years ago

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).
If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @.***> wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

hrch3n commented 3 years ago

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @.> Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).
If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @.***> wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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stegmaierj commented 3 years ago

Hi Haoran,

I just updated the XPIWIT binaries on the repository and you find the latest version here: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ . Moreover, the description of how to use the Cellpose3D XPIWIT pipeline was also updated (see https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines ). It should run smoothly with the test image “SyntheticMembranes.tif https://github.com/stegmaierj/XPIWITPipelines/blob/main/Data/SyntheticMembranes.tif” that you find in the data folder of the XPIWITPipelines repository. Just let me know if you run into any issues with that.

We’re not planning to integrate it to the original Cellpose python package, as we have a completely decoupled implementation. It’s all reimplemented in our own frameworks and extends the ideas of the original Cellpose algorithm to a full 3D version of the algorithm.

Best regards,

Johannes

On 13. Oct 2021, at 23:04, Haoran Chen @.***> wrote:

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @.> Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).

If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @.***> wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/stegmaierj/Cellpose3D/issues/1#issuecomment-942085093, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD2AA25WQHQT636DJVXGPFLUGVDGXANCNFSM5F3WKDOA. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1#issuecomment-942719496, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRLHJBOVZBPGQB7EWG3UGXX7LANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

hrch3n commented 3 years ago

Hi Johannes,

Sorry about my late response. Thanks so much for your detailed reply! I'll try to implement XPIWIT per your instructions.

Best, Haoran

From: stegmaierj @.> Sent: Friday, October 15, 2021 12:59 PM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

I just updated the XPIWIT binaries on the repository and you find the latest version here: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ . Moreover, the description of how to use the Cellpose3D XPIWIT pipeline was also updated (see https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines ). It should run smoothly with the test image “SyntheticMembranes.tif https://github.com/stegmaierj/XPIWITPipelines/blob/main/Data/SyntheticMembranes.tif” that you find in the data folder of the XPIWITPipelines repository. Just let me know if you run into any issues with that.

We’re not planning to integrate it to the original Cellpose python package, as we have a completely decoupled implementation. It’s all reimplemented in our own frameworks and extends the ideas of the original Cellpose algorithm to a full 3D version of the algorithm.

Best regards,

Johannes

On 13. Oct 2021, at 23:04, Haoran Chen @.***> wrote:

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @.> Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).

If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @.***> wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/stegmaierj/Cellpose3D/issues/1#issuecomment-942085093, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD2AA25WQHQT636DJVXGPFLUGVDGXANCNFSM5F3WKDOA. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1#issuecomment-942719496, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRLHJBOVZBPGQB7EWG3UGXX7LANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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hrch3n commented 3 years ago

Hi Johannes,

Thanks again for your detailed instructions. I'm trying to run the Linux version of XPIWIT on my Ubuntu machine and it returned the error below:

Segmentation fault (core dumped)

I was trying to run TWANGSegmentation.sh in the Example folder. Running other bash files also returned this error. May I ask if you how to fix it?

Thanks, Haoran

From: Haoran Chen @.> Sent: Wednesday, October 27, 2021 12:42 PM To: stegmaierj/Cellpose3D @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Sorry about my late response. Thanks so much for your detailed reply! I'll try to implement XPIWIT per your instructions.

Best, Haoran

From: stegmaierj @.> Sent: Friday, October 15, 2021 12:59 PM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

I just updated the XPIWIT binaries on the repository and you find the latest version here: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ . Moreover, the description of how to use the Cellpose3D XPIWIT pipeline was also updated (see https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines ). It should run smoothly with the test image “SyntheticMembranes.tif https://github.com/stegmaierj/XPIWITPipelines/blob/main/Data/SyntheticMembranes.tif” that you find in the data folder of the XPIWITPipelines repository. Just let me know if you run into any issues with that.

We’re not planning to integrate it to the original Cellpose python package, as we have a completely decoupled implementation. It’s all reimplemented in our own frameworks and extends the ideas of the original Cellpose algorithm to a full 3D version of the algorithm.

Best regards,

Johannes

On 13. Oct 2021, at 23:04, Haoran Chen @.***> wrote:

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @.> Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).

If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @.***> wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/stegmaierj/Cellpose3D/issues/1#issuecomment-942085093, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD2AA25WQHQT636DJVXGPFLUGVDGXANCNFSM5F3WKDOA. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1#issuecomment-942719496, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRLHJBOVZBPGQB7EWG3UGXX7LANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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stegmaierj commented 3 years ago

Hi Haoran,

It’s a bit difficult to debug with more information. Could you try to run XPIWIT on its own without any pipeline and look at the output you obtain on the console? Just navigate to the “Bin” folder and then try to start “./XPIWIT.sh”. You should see something like:

--

Starting XPIWIT

Processing piped arguments

--

It this already fails it would probably be a general problem with XPIWIT. If that works it’s most likely related to the input / output paths. File paths should not have any special characters or spaces contained. You can also try to open the GUI using “./XPIWITGUI.sh” and see if you can open one of the “*.sav” files from the examples folder. Then simply drag and drop the input files and folders to the input edit fields on the right hand side of the XPIWITGUI window. Maybe that works for you? If not, just let me know.

Best regards,

Johannes

Von: Haoran Chen @.> Gesendet: Mittwoch, 27. Oktober 2021 19:46 An: stegmaierj/Cellpose3D @.> Cc: Stegmaier, Johannes @.>; Comment @.> Betreff: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Thanks again for your detailed instructions. I'm trying to run the Linux version of XPIWIT on my Ubuntu machine and it returned the error below:

Segmentation fault (core dumped)

I was trying to run TWANGSegmentation.sh in the Example folder. Running other bash files also returned this error. May I ask if you how to fix it?

Thanks, Haoran

From: Haoran Chen @. <mailto:@.> > Sent: Wednesday, October 27, 2021 12:42 PM To: stegmaierj/Cellpose3D @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Sorry about my late response. Thanks so much for your detailed reply! I'll try to implement XPIWIT per your instructions.

Best, Haoran

From: stegmaierj @. <mailto:@.> > Sent: Friday, October 15, 2021 12:59 PM To: stegmaierj/Cellpose3D @. <mailto:@.> > Cc: Haoran Chen @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

I just updated the XPIWIT binaries on the repository and you find the latest version here: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ . Moreover, the description of how to use the Cellpose3D XPIWIT pipeline was also updated (see https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines ). It should run smoothly with the test image “SyntheticMembranes.tif https://github.com/stegmaierj/XPIWITPipelines/blob/main/Data/SyntheticMembranes.tif” that you find in the data folder of the XPIWITPipelines repository. Just let me know if you run into any issues with that.

We’re not planning to integrate it to the original Cellpose python package, as we have a completely decoupled implementation. It’s all reimplemented in our own frameworks and extends the ideas of the original Cellpose algorithm to a full 3D version of the algorithm.

Best regards,

Johannes

On 13. Oct 2021, at 23:04, Haoran Chen @. <mailto:@.> > wrote:

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @. <mailto:@.> > Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @. <mailto:@.> > Cc: Haoran Chen @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).

If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @. <mailto:@.> > wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

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hrch3n commented 3 years ago

Thanks so much for your prompt reply! I ran ./XPIWIT.sh and ./XPIWITGUI.sh directly and both returned:

Segmentation fault (core dumped)

It's the same error I got when I ran .sh files in the Examples folder. I guess it might be a general problem as you said?

Best, Haoran

From: stegmaierj @.> Sent: Thursday, October 28, 2021 3:54 AM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

It’s a bit difficult to debug with more information. Could you try to run XPIWIT on its own without any pipeline and look at the output you obtain on the console? Just navigate to the “Bin” folder and then try to start “./XPIWIT.sh”. You should see something like:

--

Starting XPIWIT

Processing piped arguments

--

It this already fails it would probably be a general problem with XPIWIT. If that works it’s most likely related to the input / output paths. File paths should not have any special characters or spaces contained. You can also try to open the GUI using “./XPIWITGUI.sh” and see if you can open one of the “*.sav” files from the examples folder. Then simply drag and drop the input files and folders to the input edit fields on the right hand side of the XPIWITGUI window. Maybe that works for you? If not, just let me know.

Best regards,

Johannes

Von: Haoran Chen @.> Gesendet: Mittwoch, 27. Oktober 2021 19:46 An: stegmaierj/Cellpose3D @.> Cc: Stegmaier, Johannes @.>; Comment @.> Betreff: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Thanks again for your detailed instructions. I'm trying to run the Linux version of XPIWIT on my Ubuntu machine and it returned the error below:

Segmentation fault (core dumped)

I was trying to run TWANGSegmentation.sh in the Example folder. Running other bash files also returned this error. May I ask if you how to fix it?

Thanks, Haoran

From: Haoran Chen @. <mailto:@.> > Sent: Wednesday, October 27, 2021 12:42 PM To: stegmaierj/Cellpose3D @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Sorry about my late response. Thanks so much for your detailed reply! I'll try to implement XPIWIT per your instructions.

Best, Haoran

From: stegmaierj @. <mailto:@.> > Sent: Friday, October 15, 2021 12:59 PM To: stegmaierj/Cellpose3D @. <mailto:@.> > Cc: Haoran Chen @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

I just updated the XPIWIT binaries on the repository and you find the latest version here: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ . Moreover, the description of how to use the Cellpose3D XPIWIT pipeline was also updated (see https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines ). It should run smoothly with the test image “SyntheticMembranes.tif https://github.com/stegmaierj/XPIWITPipelines/blob/main/Data/SyntheticMembranes.tif” that you find in the data folder of the XPIWITPipelines repository. Just let me know if you run into any issues with that.

We’re not planning to integrate it to the original Cellpose python package, as we have a completely decoupled implementation. It’s all reimplemented in our own frameworks and extends the ideas of the original Cellpose algorithm to a full 3D version of the algorithm.

Best regards,

Johannes

On 13. Oct 2021, at 23:04, Haoran Chen @. <mailto:@.> > wrote:

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @. <mailto:@.> > Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @. <mailto:@.> > Cc: Haoran Chen @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).

If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @. <mailto:@.> > wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 &mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub &referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

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stegmaierj commented 3 years ago

Alright, jop that sounds like a general problem. One thing you could try is to check permissions of all files, e.g., by changing the permissions to “755” or even “777” for all files contained in the XPIWIT folder. In some cases we had the issue that an antivirus software was blocking the software from executing. And finally, it could be that the system you’re using is not compatible with the compiled binary. You could also try to use one of the older releases and see if one of these works for you.

If none of these works, the best way would be if you recompile XPIWIT from scratch using the code you find in the repository. There are also instructions on this found in the documentation provided in binary packages (folder "Documentation”), so you may want to have a look at this. If you plan to implement your own code, you’d have to recompile XPIWIT on your own anyway.

Alternatively, you could also try to run the software using a virutual machine with Windows or MacOS installed, just to try if it suits your needs at all and would be worth the effort recompiling it.

Hope any of these suggestions helps?

Best regards,

Johannes

On 28. Oct 2021, at 16:18, Haoran Chen @.***> wrote:

Thanks so much for your prompt reply! I ran ./XPIWIT.sh and ./XPIWITGUI.sh directly and both returned:

Segmentation fault (core dumped)

It's the same error I got when I ran .sh files in the Examples folder. I guess it might be a general problem as you said?

Best, Haoran

From: stegmaierj @.> Sent: Thursday, October 28, 2021 3:54 AM To: stegmaierj/Cellpose3D @.> Cc: Haoran Chen @.>; Author @.> Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

It’s a bit difficult to debug with more information. Could you try to run XPIWIT on its own without any pipeline and look at the output you obtain on the console? Just navigate to the “Bin” folder and then try to start “./XPIWIT.sh”. You should see something like:

--

Starting XPIWIT

Processing piped arguments

--

It this already fails it would probably be a general problem with XPIWIT. If that works it’s most likely related to the input / output paths. File paths should not have any special characters or spaces contained. You can also try to open the GUI using “./XPIWITGUI.sh” and see if you can open one of the “*.sav” files from the examples folder. Then simply drag and drop the input files and folders to the input edit fields on the right hand side of the XPIWITGUI window. Maybe that works for you? If not, just let me know.

Best regards,

Johannes

Von: Haoran Chen @.> Gesendet: Mittwoch, 27. Oktober 2021 19:46 An: stegmaierj/Cellpose3D @.> Cc: Stegmaier, Johannes @.>; Comment @.> Betreff: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Thanks again for your detailed instructions. I'm trying to run the Linux version of XPIWIT on my Ubuntu machine and it returned the error below:

Segmentation fault (core dumped)

I was trying to run TWANGSegmentation.sh in the Example folder. Running other bash files also returned this error. May I ask if you how to fix it?

Thanks, Haoran

From: Haoran Chen @. <mailto:@.> > Sent: Wednesday, October 27, 2021 12:42 PM To: stegmaierj/Cellpose3D @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Johannes,

Sorry about my late response. Thanks so much for your detailed reply! I'll try to implement XPIWIT per your instructions.

Best, Haoran

From: stegmaierj @. <mailto:@.> > Sent: Friday, October 15, 2021 12:59 PM To: stegmaierj/Cellpose3D @. <mailto:@.> > Cc: Haoran Chen @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Hi Haoran,

I just updated the XPIWIT binaries on the repository and you find the latest version here: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ . Moreover, the description of how to use the Cellpose3D XPIWIT pipeline was also updated (see https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines ). It should run smoothly with the test image “SyntheticMembranes.tif https://github.com/stegmaierj/XPIWITPipelines/blob/main/Data/SyntheticMembranes.tif” that you find in the data folder of the XPIWITPipelines repository. Just let me know if you run into any issues with that.

We’re not planning to integrate it to the original Cellpose python package, as we have a completely decoupled implementation. It’s all reimplemented in our own frameworks and extends the ideas of the original Cellpose algorithm to a full 3D version of the algorithm.

Best regards,

Johannes

On 13. Oct 2021, at 23:04, Haoran Chen @. <mailto:@.> > wrote:

Hi Johannes,

Thanks for your reply. I just want to apply pretrained models on test data so I will try XPIWIT per your instruction.

May I ask if you are planning to integrate Cellpose3D into the Cellpose python package?

Best, Haoran

From: stegmaierj @. <mailto:@.> > Sent: Wednesday, October 13, 2021 5:01 AM To: stegmaierj/Cellpose3D @. <mailto:@.> > Cc: Haoran Chen @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [stegmaierj/Cellpose3D] How to apply pretrained model? (#1)

Dear Haoran,

thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software?

Options are:

If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed).

If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks.

Best regards,

Johannes

On 13. Oct 2021, at 00:05, Haoran Chen @. <mailto:@.> > wrote:

Hi,

I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks?

Thanks, Haoran

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stegmaierj/Cellpose3D/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 &mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub &referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

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saskra commented 3 years ago

Same problem here:

saskra@a:~/PycharmProjects/XPIWITPipelines/2021_10_15_XPIWIT_Ubuntu_x64/Bin$ ./XPIWIT.sh
Segmentation fault (core dumped)
saskra@a:~/PycharmProjects/XPIWITPipelines/2021_10_15_XPIWIT_Ubuntu_x64/Bin$ ./XPIWIT
./XPIWIT: error while loading shared libraries: libc10.so: cannot open shared object file: No such file or directory

stegmaierj commented 3 years ago

Alright, that definitely looks weird. Could you provide some more details on the system / OS version you‘re trying to run it on? This would potentially help to reproduce the error.

Thanks!

saskra commented 3 years ago

It's Ubuntu 18.04.6 LTS (GNU/Linux 4.15.0-161-generic x86_64).

By the way, it works under Windows, but there I have the weaker hardware. In addition, it also breaks there when I replace the sample files with my own - but I'd better open a separate issue for that.

saskra commented 3 years ago

It works on Ubuntu 20.04.3 LTS.

postnubilaphoebus commented 10 months ago

Hello, I have a similar issue. It is linked here: https://github.com/stegmaierj/XPIWITPipelines/issues/2. After making the file executable, I get Inconsistency detected by ld.so: dl-call-libc-early-init.c: 37: _dl_call_libc_early_init: Assertion "sym != NULL'"failed!

ivanmag22 commented 1 month ago

Hi, about Python implementation is there a pretrained model?

Dear Haoran, thanks for your message and your interest in our implementations – we’re currently still working on some more documentation and integration to other tools and would provide you some more information on how to use it soon. May I ask how you’d like to use the software? Options are: 1. If you want to use the Python implementation to train your own models, I would have to refer you to a colleague (Dennis Eschweiler, CC’ed). 2. If you just want to apply pretrained models that can be easily accomplished via XPIWIT, a software tool we developed for this or via MorphoGraphX that also soon includes the Cellpose3D algorithm in the latest release. However, we still need to prepare a new release for this, such that it may be used by others. For now, see here for downloading XPIWIT: https://bitbucket.org/jstegmaier/xpiwit/downloads/ https://bitbucket.org/jstegmaier/xpiwit/downloads/ and here for a collection of pipelines https://github.com/stegmaierj/XPIWITPipelines https://github.com/stegmaierj/XPIWITPipelines . The latter site is still under construction and not very informative yet, but we’ll try to fill it in the next couple of days/weeks. Best regards, Johannes … On 13. Oct 2021, at 00:05, Haoran Chen @.***> wrote: Hi, I'm a member of the HuBMAP CMU TC team. I'd like to test this great work on 3D Image Mass Cytometry (3D) images, but I didn't see the manual/instruction as Cellpose has. Would you please walk me through how to apply the pretrained Cellpose3D model on a 3D image to generate segmentation masks? Thanks, Haoran — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHOCRI65IYUZG6Y6EYQ2TLUGSWJVANCNFSM5F3WKDOA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

stegmaierj commented 1 month ago

Hi ivanmag22,

jop there is a checkpoint available in the repository. If you apply the model using apply_network.py, it automatically loads the provided checkpoint by default (epoch=999.ckpt).

Otherwise, if you want to use XPIWIT to just apply the model to some data, see here for some more details. There is a pretrained model contained in the Cellpose3D.pt file that can be loaded by XPIWIT and used for processing.

Hope this helps?

Best regards,

Johannes

stegmaierj / Cellpose3D

How to apply pretrained model? #1