tractography of histological data
Hello, we are working with low level image processing libraries for histological data (either doingstructure tensor from light sheet neuronal tracts images, or even more complicated glial directions from 2D stacks of H&E). From previous mails I have read "expanding tractography to non MRI data". Where you referring to something like this? For the moment we are using the matlab code of Schurr and Mezer https://github.com/MezerLab/NisslST/tree/v1.0but we indeed are working on the porting. Anybody else doing something like this? Is this within the plan of Dipy? Best,Alex
Hello, Yes, we were referring to something like your project. We are interested in generalizing our tractography framework. Recently, we had a request to do tractography on ophthalmology data. It would be great if you can tell us more during DIPY OFFICE HOURS. Can you block a spot in our dipy office hours spreadsheet here: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Also, everyone can book a spot to DIPY Office Hours! Do not hesitate if you have any questions about your code, reconstruction model selection or preprocessing! If you want to start a collaboration, this is also a good place to start. DIPY Office Hours booking link: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Serge K On Thu, Jan 19, 2023 at 3:32 PM Alex Crimi via DIPY <dipy@python.org> wrote:
We have some PLI data (also matching DTI and histology), but for the moment we want to believe myelin has a direction (with or without NISSL staining), we have a dream we still have a dream.If you can catch myelin direction only with NISSL staining, then we are wrong but we tried. The time slots at 1-2 pm Eastern time are really bad for us. Could we propose something earlier? Ale On Tuesday, January 24, 2023 at 09:46:02 PM GMT+1, roberto toro <roberto.toro@gmail.com> wrote: Hola,We'll be also working on that. Vaibhav Sahu in our lab has started looking at the structor tensor approach, and we're also starting to collect PLI data. Would love to discuss further!cheers,roberto On Jan 24 2023, at 5:03 pm, Serge K. <skab12@gmail.com> wrote: Hello, Yes, we were referring to something like your project. We are interested in generalizing our tractography framework. Recently, we had a request to do tractography on ophthalmology data. It would be great if you can tell us more during DIPY OFFICE HOURS. Can you block a spot in our dipy office hours spreadsheet here: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Also, everyone can book a spot to DIPY Office Hours! Do not hesitate if you have any questions about your code, reconstruction model selection or preprocessing! If you want to start a collaboration, this is also a good place to start. DIPY Office Hours booking link: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Serge K On Thu, Jan 19, 2023 at 3:32 PM Alex Crimi via DIPY <dipy@python.org> wrote: Hello, we are working with low level image processing libraries for histological data (either doingstructure tensor from light sheet neuronal tracts images, or even more complicated glial directions from 2D stacks of H&E). From previous mails I have read "expanding tractography to non MRI data". Where you referring to something like this? For the moment we are using the matlab code of Schurr and Mezer https://github.com/MezerLab/NisslST/tree/v1.0but we indeed are working on the porting. Anybody else doing something like this? Is this within the plan of Dipy? Best,Alex_______________________________________________DIPY mailing list -- dipy@python.orgTo unsubscribe send an email to dipy-leave@python.orghttps://mail.python.org/mailman3/lists/dipy.python.org/Member address: skab12@gmail.com _______________________________________________DIPY mailing list -- dipy@python.orgTo unsubscribe send an email to dipy-leave@python.orghttps://mail.python.org/mailman3/lists/dipy.python.org/Member address: roberto.toro@gmail.com
The time slots at 1-2 pm Eastern time are really bad for us. Could we propose something earlier?
Sure, I just added 2 time slots: 9:30am and 10:30am ET. Here is the updated document: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... These 2 new time slots should be convenient for our European and South Asia community. Serge K ------------------------------ On Tue, Jan 24, 2023 at 4:43 PM Alex Crimi <alex.crimi@yahoo.com> wrote:
Hello, Yes, we were referring to something like your project. We are interested in generalizing our tractography framework. Recently, we had a request to do tractography on ophthalmology data. It would be great if you can tell us more during DIPY OFFICE HOURS. Can you block a spot in our dipy office hours spreadsheet here: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Also, everyone can book a spot to DIPY Office Hours! Do not hesitate if you have any questions about your code, reconstruction model selection or preprocessing! If you want to start a collaboration, this is also a good place to start. DIPY Office Hours booking link: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Serge K On Thu, Jan 19, 2023 at 3:32 PM Alex Crimi via DIPY <dipy@python.org> wrote:
We have some PLI data (also matching DTI and histology), but for the moment we want to believe myelin has a direction (with or without NISSL staining), we have a dream we still have a dream.If you can catch myelin direction only with NISSL staining, then we are wrong but we tried. The time slots at 1-2 pm Eastern time are really bad for us. Could we propose something earlier? Ale On Tuesday, January 24, 2023 at 09:46:02 PM GMT+1, roberto toro <roberto.toro@gmail.com> wrote: Hola,We'll be also working on that. Vaibhav Sahu in our lab has started looking at the structor tensor approach, and we're also starting to collect PLI data. Would love to discuss further!cheers,roberto On Jan 24 2023, at 5:03 pm, Serge K. <skab12@gmail.com> wrote: Hello, Yes, we were referring to something like your project. We are interested in generalizing our tractography framework. Recently, we had a request to do tractography on ophthalmology data. It would be great if you can tell us more during DIPY OFFICE HOURS. Can you block a spot in our dipy office hours spreadsheet here: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Also, everyone can book a spot to DIPY Office Hours! Do not hesitate if you have any questions about your code, reconstruction model selection or preprocessing! If you want to start a collaboration, this is also a good place to start. DIPY Office Hours booking link: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... Serge K On Thu, Jan 19, 2023 at 3:32 PM Alex Crimi via DIPY <dipy@python.org> wrote: Hello, we are working with low level image processing libraries for histological data (either doingstructure tensor from light sheet neuronal tracts images, or even more complicated glial directions from 2D stacks of H&E). From previous mails I have read "expanding tractography to non MRI data". Where you referring to something like this? For the moment we are using the matlab code of Schurr and Mezer https://github.com/MezerLab/NisslST/tree/v1.0but we indeed are working on the porting. Anybody else doing something like this? Is this within the plan of Dipy? Best,Alex_______________________________________________DIPY mailing list -- dipy@python.orgTo unsubscribe send an email to dipy-leave@python.orghttps://mail.python.org/mailman3/lists/dipy.python.org/Member address: skab12@gmail.com _______________________________________________DIPY mailing list -- dipy@python.orgTo unsubscribe send an email to dipy-leave@python.orghttps://mail.python.org/mailman3/lists/dipy.python.org/Member address: roberto.toro@gmail.com
The time slots at 1-2 pm Eastern time are really bad for us. Could we propose something earlier?
Sure, I just added 2 time slots: 9:30am and 10:30am ET. Here is the updated document: https://docs.google.com/spreadsheets/d/1IVaixEbjKQqS2MrZHw1L2Gso8a0GannT19Gw... These 2 new time slots should be convenient for our European and South Asia community. Serge K ------------------------------ On Tue, Jan 24, 2023 at 4:43 PM Alex Crimi <alex.crimi@yahoo.com> wrote:
participants (3)
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Alex Crimi -
roberto toro -
Serge K.