Closed jiyuuchc closed 6 months ago
Hello @jiyuuchc
We wrote a TrackMate detector plugin. This is a deep learning based cell detector, originally developed for a local hematology research project, but we are considering releasing it to the public. While Trackmate already includes several cell-detector options, some users might still find our alternative useful due to its speed.
Awesome! We really built TrackMate so that it can be extended by others, and this issue makes my day! I can't wait to study the technology you used to communicate with Python.
So before we upload it to image.net, we would like to double check with the upstream to see if there is any recommended "best-practice" for doing this, e.g., just off the top of my head:
- Package name: we currently use ij.plugin.trackmate.lacss, which in theory could lead to collision. Should we change that?
I would recommend using the same root that of the TrackMate packages, though:
fiji.plugin.trackmate.detection.lacss
so that it fits nicely under the same package hierarchy common to all detectors.
- Artifact name. Any conventions?
We recommend TrackMate-Something
, with a capital 'S'. See for instance the artifact names for the other extensions:
https://github.com/orgs/trackmate-sc/repositories
- Is it ok to hijack trackmate's mailing list tag, e.g. https://forum.image.sc/tag/trackmate, for the plugin's POM metadata?
Totally ok.
- Anything else?
We are working on a v8 version, that will support 3D segmentation. This will cause major changes in the API that might affect you. Check the draft PR for a succint description of what will happen: https://github.com/trackmate-sc/TrackMate/pull/263
But in any case we will be there to help with porting your code to the future new v8, to be out probably early next year or for Christmas.
Did a quick scan of #263. It seems that the API changes are relatively minor. We would like to aim for a synchronized release. I assume the v8 branch is the one we should track for our own developmental branch?
From: Jean-Yves Tinevez @.***> Sent: Tuesday, November 21, 2023 3:53 AM To: trackmate-sc/TrackMate Cc: Yu,Ji; Mention Subject: Re: [trackmate-sc/TrackMate] Recommendations for plugins (Issue #282)
Attention: This is an external email. Use caution responding, opening attachments or clicking on links.
We wrote a TrackMate detector pluginhttps://urldefense.com/v3/__https://github.com/jiyuuchc/TrackMate-Lacss/__;!!Cn_UX_p3!nbBL8ZrnXbHdisd4jqFMuDR7pbH_P01JlogCmwGLkO2f02kxnzj-EEK2w0JK_EHp8zH-IflnxejXCHkqx13vEw$. This is a deep learning based cell detector, originally developed for a local hematology research project, but we are considering releasing it to the public. While Trackmate already includes several cell-detector options, some users might still find our alternative useful due to its speedhttps://urldefense.com/v3/__https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10243149__;!!Cn_UX_p3!nbBL8ZrnXbHdisd4jqFMuDR7pbH_P01JlogCmwGLkO2f02kxnzj-EEK2w0JK_EHp8zH-IflnxejXCHmP2_e6dg$.
Awesome! We really built TrackMate so that it cab extended by others, and this issue makes my day! I can't wait to study the technology you used to communicate with Python.
So before we upload it to image.net, we would like to double check with the upstream to see if there is any recommended "best-practice" for doing this, e.g., just off the top of my head:
I would recommend using the same root that of the TrackMate packages, though: fiji.plugin.trackmate.detection.lacss
so that it fits nicely under the same package hierarchy common to all detectors.
We recommend TrackMate-Something, with a capital 'S'. See for instance the artifact names for the other extensions: https://github.com/orgs/trackmate-sc/repositorieshttps://urldefense.com/v3/__https://github.com/orgs/trackmate-sc/repositories__;!!Cn_UX_p3!nbBL8ZrnXbHdisd4jqFMuDR7pbH_P01JlogCmwGLkO2f02kxnzj-EEK2w0JK_EHp8zH-IflnxejXCHkm6MiarA$
Totally ok.
We are working on a v8 version, that will support 3D segmentation. This will cause major changes in the API that might affect you. Check the draft PR for a succint description of what will happen:
But in any case we will be there to help with porting your code to the future new v8, to be out probably early next year or for Christmas.
— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/trackmate-sc/TrackMate/issues/282*issuecomment-1820484663__;Iw!!Cn_UX_p3!nbBL8ZrnXbHdisd4jqFMuDR7pbH_P01JlogCmwGLkO2f02kxnzj-EEK2w0JK_EHp8zH-IflnxejXCHnXb7x5CQ$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAKRPNWO5RG5O6MMDRHIMWDYFRTWZAVCNFSM6AAAAAA7TRCX52VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRQGQ4DINRWGM__;!!Cn_UX_p3!nbBL8ZrnXbHdisd4jqFMuDR7pbH_P01JlogCmwGLkO2f02kxnzj-EEK2w0JK_EHp8zH-IflnxejXCHlxQmip-w$. You are receiving this because you were mentioned.Message ID: @.***>
Yes absolutely. Anything else? Can I close this issue?
Certainly. Thanks for the reply.
Ji
From: Jean-Yves Tinevez @.***> Sent: Wednesday, February 7, 2024 8:36 AM To: trackmate-sc/TrackMate Cc: Yu,Ji; Mention Subject: Re: [trackmate-sc/TrackMate] Recommendations for plugins (Issue #282)
Attention: This is an external email. Use caution responding, opening attachments or clicking on links.
Yes absolutely. Anything else? Can I close this issue?
— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/trackmate-sc/TrackMate/issues/282*issuecomment-1932066345__;Iw!!Cn_UX_p3!kTBHXFJ7ispYsP5EAxtSn_mOzFXo-Kh9tgMzdBR87eF5Ju03viptAQmhn_QoDpyiJ1cyFVDPZW8y1pReH44m6A$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAKRPNVYPLXTLOIMDSPS3VLYSN7MLAVCNFSM6AAAAAA7TRCX52VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZSGA3DMMZUGU__;!!Cn_UX_p3!kTBHXFJ7ispYsP5EAxtSn_mOzFXo-Kh9tgMzdBR87eF5Ju03viptAQmhn_QoDpyiJ1cyFVDPZW8y1pS45SYmxw$. You are receiving this because you were mentioned.Message ID: @.***>
We wrote a TrackMate detector plugin. This is a deep learning based cell detector, originally developed for a local hematology research project, but we are considering releasing it to the public.
While Trackmate already includes several cell-detector options, some users might still find our alternative useful due to its speed.
So before we upload it to image.net, we would like to double check with the upstream to see if there is any recommended "best-practice" for doing this, e.g., just off the top of my head: