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shlizee / C-elegans-Neural-Interactome

Realtime simulation and visualization of neural dynamics of a full nervous system (C. elegans).
http://neuralcode.amath.washington.edu/neuralinteractome
BSD 3-Clause "New" or "Revised" License
34 stars 8 forks source link

structure of the saved_dynamics.npy file #3

Closed luissmayorga closed 5 years ago

luissmayorga commented 5 years ago

Would you please provide the headers for the columns and rows of the saved_dynamics.npy file? Thanks Luis

jimin9292 commented 5 years ago

Dear Luis

Thank you for raising this issue! The rows and columns of the saved_dynamics.npy are "timepoints" and "neurons' indices". Each row corresponds to individual time point in 0.01 seconds (10ms) resolution. i.e. row 1 = 0s, row 2 = 0.01s, row 3 = 0.02s ...

Columns are neurons which is ordered from head to tail direction. I added the 'neuron_names.txt' which shows the neurons' names in this order.

I also found out that there was a small bug when saving the 'saved_dynamics.npy' which results in incorrect voltage values. I just pushed the updated version of the application which fixes this issue. So please update your local installation with the new version!

Thank you, and let me know if you have any question

Jimin

luissmayorga commented 5 years ago

Thanks Jimin, I will be in touch, Luis

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El mié., 17 jul. 2019 a las 19:04, jimin9292 (notifications@github.com) escribió:

Dear Luis

Thank you for raising this issue! The rows and columns of the saved_dynamics.npy are "timepoints" and "neurons' indices". Each row corresponds to individual time point in 0.01 seconds (10ms) resolution. i.e. row 1 = 0s, row 2 = 0.01s, row 3 = 0.02s ...

Columns are neurons which is ordered from head to tail direction. I added the 'neuron_names.txt' which shows the neurons' names in this order.

I also found out that there was a small bug when saving the 'saved_dynamics.npy' which results in incorrect voltage values. I just pushed the updated version of the application which fixes this issue. So please update your local installation with the new version!

Thank you, and let me know if you have any question

Jimin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/shlizee/C-elegans-Neural-Interactome/issues/3?email_source=notifications&email_token=AFK4S7USESL6ALQY4FDFPNLP76JO5A5CNFSM4IEQHYS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GXBYA#issuecomment-512585952, or mute the thread https://github.com/notifications/unsubscribe-auth/AFK4S7VHIQUPY6B4OOSEYILP76JO5ANCNFSM4IEQHYSQ .

-- Luis S. Mayorga Ph.D. Investigador Superior (CONICET) Profesor Titular, Bioenergética (FCEN-UN Cuyo) Casilla de Correo 56 5500 Mendoza, Argentina tel 54-261-4054843 interno 7014

luissmayorga commented 5 years ago

Dear Jimin, This is an example of a run. It is extremely important that the columns correspond to specific neurons (obviously). Since we will start analyzing several conditions, would you please corroborate that I have got the correct order for the neurons? Thanks Luis

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El mié., 17 jul. 2019 a las 19:04, jimin9292 (notifications@github.com) escribió:

Dear Luis

Thank you for raising this issue! The rows and columns of the saved_dynamics.npy are "timepoints" and "neurons' indices". Each row corresponds to individual time point in 0.01 seconds (10ms) resolution. i.e. row 1 = 0s, row 2 = 0.01s, row 3 = 0.02s ...

Columns are neurons which is ordered from head to tail direction. I added the 'neuron_names.txt' which shows the neurons' names in this order.

I also found out that there was a small bug when saving the 'saved_dynamics.npy' which results in incorrect voltage values. I just pushed the updated version of the application which fixes this issue. So please update your local installation with the new version!

Thank you, and let me know if you have any question

Jimin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/shlizee/C-elegans-Neural-Interactome/issues/3?email_source=notifications&email_token=AFK4S7USESL6ALQY4FDFPNLP76JO5A5CNFSM4IEQHYS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GXBYA#issuecomment-512585952, or mute the thread https://github.com/notifications/unsubscribe-auth/AFK4S7VHIQUPY6B4OOSEYILP76JO5ANCNFSM4IEQHYSQ .

-- Luis S. Mayorga Ph.D. Investigador Superior (CONICET) Profesor Titular, Bioenergética (FCEN-UN Cuyo) Casilla de Correo 56 5500 Mendoza, Argentina tel 54-261-4054843 interno 7014

jimin9292 commented 5 years ago

Hi Luis

It seems like the attachment leads to AVG virus download page for me? Is it possible you attach the file directly either here or email?

luissmayorga commented 5 years ago

Sorry about that, I print to a pdf the first page. If it is correct, I assume the rest should be OK. Thanks again Luis

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El vie., 19 jul. 2019 a las 22:53, jimin9292 (notifications@github.com) escribió:

Hi Luis

It seems like the attachment leads to AVG virus download page for me? Is it possible you attach the file directly either here or email?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/shlizee/C-elegans-Neural-Interactome/issues/3?email_source=notifications&email_token=AFK4S7T3AMJW6IXP4EWGIP3QAJVWZA5CNFSM4IEQHYS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2NEBXY#issuecomment-513425631, or mute the thread https://github.com/notifications/unsubscribe-auth/AFK4S7XH6HKVZRMMXSM3U2TQAJVWZANCNFSM4IEQHYSQ .

-- Luis S. Mayorga Ph.D. Investigador Superior (CONICET) Profesor Titular, Bioenergética (FCEN-UN Cuyo) Casilla de Correo 56 5500 Mendoza, Argentina tel 54-261-4054843 interno 7014

jimin9292 commented 5 years ago

I am still unable to see the content (the link keeps leading to AVG antivirus page). Is there something I am missing here? or is it possible to send me the example of the run to my email? (jk55@u.washington.edu)