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Problem doing ALF conversion on phy sorted files which have merged or split clusters #308

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antaramaj16 opened this issue May 18, 2022 · 4 comments

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antaramaj16 commented May 18, 2022

For ephys sessions that have been phy curated and there are spikes either merged or split - while converting into ALF files you may run into this error:

How exactly do we resolve this because a lot of our sessions for analysis have already been phy sorted and normally it doesn't give us problems if we don't merge or split clusters?

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oliche commented Jun 2, 2022

Hi,
Yes it is probable since exporting after manual curation is not something we are super familiar with.
Would you mind sharing the dataset with us so we can reproduce this locally ?

If you do not want to post the dataset publicly, you can contact me by email or at [email protected]

Author

antaramaj16 commented Jun 3, 2022 via email

Hi, Please find attached the dataset for a session. Thank you! Sincerely, Antara amplitudes.npy <https://drive.google.com/file/d/1rG7tFTWHUJllMziL7Hb7kVKZ7Im3UZEO/view?usp=drive_web> channel_map.npy <https://drive.google.com/file/d/15gLPJ70YCY0gFQqhBdV_kKqHz9XkC_7-/view?usp=drive_web> channel_positions.npy <https://drive.google.com/file/d/1slz5e3oVdA64qqPYQnm22er5YG8OdBzh/view?usp=drive_web> cluster_Amplitude.tsv <https://drive.google.com/file/d/1FQi1PI3oD1wGD_eC2MblJzThCmDFOiTZ/view?usp=drive_web> cluster_ContamPct.tsv <https://drive.google.com/file/d/1tQ-k8_nWCBnGZy4pUZnEO5kZGHDwQk0m/view?usp=drive_web> cluster_group.tsv <https://drive.google.com/file/d/1Fvg0lOTm5JhtYCObJCKQ5ko0av86TXaZ/view?usp=drive_web> cluster_info.tsv <https://drive.google.com/file/d/12LXsBh1HPTXHmIR6P5KPn3qDCLLM0wAT/view?usp=drive_web> cluster_KSLabel.tsv <https://drive.google.com/file/d/1XmQ_LO16bQimNSRvnuCzu6Uw35mRz1sx/view?usp=drive_web> params.py <https://drive.google.com/file/d/1I9gZuxjl_T4N8e0pX6GFn-GrAhiJAA4Q/view?usp=drive_web> phy.log <https://drive.google.com/file/d/1XnXZCC4XtEmDaxNFpr-Dtl9tmk_xzz0_/view?usp=drive_web> rez.mat <https://drive.google.com/file/d/11k3b9YuF238gGjhn_0PvDUWOIMU-9N3r/view?usp=drive_web> similar_templates.npy <https://drive.google.com/file/d/1LLJ3UFwDH7OfeHrLMA0Upi6TK-y2r7P7/view?usp=drive_web> spike_clusters.npy <https://drive.google.com/file/d/1JDgeb-A39dJ8VfdFYu__bChWWeEagRAP/view?usp=drive_web> spike_templates.npy <https://drive.google.com/file/d/1DC8ZuVfyEtBy0VGVZ6--rYB-m_dmnMjK/view?usp=drive_web> spike_times.npy <https://drive.google.com/file/d/1JZ7MMVIDZ7jQJw7bb3d8C0FSZ1kFem7n/view?usp=drive_web> templates.npy <https://drive.google.com/file/d/1JZQ1XkkcsbzqxBkOXhbjsnxXCfAPZzoU/view?usp=drive_web> templates_ind.npy <https://drive.google.com/file/d/1nQmFoLNpZPiEOG-EBLdwxOo1jlfMQOwd/view?usp=drive_web> whitening_mat.npy <https://drive.google.com/file/d/10Pdj2LxK5WsSFu1X18GnBCz-YaDBpKZz/view?usp=drive_web> whitening_mat_inv.npy <https://drive.google.com/file/d/1EC3zKVck4JV1X_qh4oWBjGa4zs7xLJem/view?usp=drive_web>

On Thu, Jun 2, 2022 at 8:12 AM Olivier Winter ***@***.***> wrote: Hi, Yes it is probable since exporting after manual curation is not something we are super familiar with. Would you mind sharing the dataset with us so we can reproduce this locally ? If you do not want to post the dataset publicly, you can contact me by email or at ***@***.*** — Reply to this email directly, view it on GitHub <#308 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARV7RIU5TK7GCU4UKIO7KGTVNBND7ANCNFSM5WI7F6YA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *_____* *Antara Majumdar* DPhil Physiology, Anatomy and Genetics | Kellogg College University of Oxford | Lak Lab Department of Physiology, Anatomy and Genetics Sherrington Building, Sherrington Rd, Oxford OX1 3PT Tel: +44 07709252462

Author

antaramaj16 commented Jun 3, 2022 via email

Here are the raw files: 2022-05-06_AMR019_g0_t0.imec0.lf.bin <https://drive.google.com/file/d/18JLlyIse9rJJzbPx1u8du9oHgTJshlpV/view?usp=drive_web> 2022-05-06_AMR019_g0_t0.imec0.lf.meta <https://drive.google.com/file/d/1z7yGkgrSbHCM-_bsOT-lvG-nSooaW3rZ/view?usp=drive_web> 2022-05-06_AMR019_g0_t0.nidq.bin <https://drive.google.com/file/d/1Im1IMgznuG8rX6FAfMoSnpS_2hTNGg7R/view?usp=drive_web> 2022-05-06_AMR019_g0_t0.nidq.meta <https://drive.google.com/file/d/1cAOfiIn8s3Q_1Si3qfO41qqHravW--wH/view?usp=drive_web> 2022-05-06_AMR019_g0_tcat.imec0.ap.bin <https://drive.google.com/file/d/1akcPg8RkGPC57teMLVoAMA_vh5ifAm9U/view?usp=drive_web> 2022-05-06_AMR019_g0_tcat.imec0.ap.meta <https://drive.google.com/file/d/1-Z1xzKrEgfE4jP_k5BX2dA0matARgmTA/view?usp=drive_web> 2022-05-06_AMR019_g0_tcat.imec0.ap.SY_384_6_500... <https://drive.google.com/file/d/1TZofXCeJ0mgOhpCUXUDzrDMiEkFsgs8H/view?usp=drive_web> 2022-05-06_AMR019_g0_tcat.nidq.meta <https://drive.google.com/file/d/1yn1JDk5ODvkjya1h-DOD7CQNWfcs6T9p/view?usp=drive_web> 2022-05-06_AMR019_g0_tcat.nidq.XA_0_0.txt <https://drive.google.com/file/d/1UkNW9f4Wiyl0Eert4IZ0mfMAZEzMk3cG/view?usp=drive_web> 2022-05-06_AMR019_g0_tcat.nidq.XA_1_500.txt <https://drive.google.com/file/d/1CymsBh_X2ZMXY_2OvLpw1w7VDoOIRy-E/view?usp=drive_web> On Fri, Jun 3, 2022 at 10:59 AM Antara Majumdar ***@***.***> wrote:

Hi, Please find attached the dataset for a session. Thank you! Sincerely, Antara amplitudes.npy <https://drive.google.com/file/d/1rG7tFTWHUJllMziL7Hb7kVKZ7Im3UZEO/view?usp=drive_web> channel_map.npy <https://drive.google.com/file/d/15gLPJ70YCY0gFQqhBdV_kKqHz9XkC_7-/view?usp=drive_web> channel_positions.npy <https://drive.google.com/file/d/1slz5e3oVdA64qqPYQnm22er5YG8OdBzh/view?usp=drive_web> cluster_Amplitude.tsv <https://drive.google.com/file/d/1FQi1PI3oD1wGD_eC2MblJzThCmDFOiTZ/view?usp=drive_web> cluster_ContamPct.tsv <https://drive.google.com/file/d/1tQ-k8_nWCBnGZy4pUZnEO5kZGHDwQk0m/view?usp=drive_web> cluster_group.tsv <https://drive.google.com/file/d/1Fvg0lOTm5JhtYCObJCKQ5ko0av86TXaZ/view?usp=drive_web> cluster_info.tsv <https://drive.google.com/file/d/12LXsBh1HPTXHmIR6P5KPn3qDCLLM0wAT/view?usp=drive_web> cluster_KSLabel.tsv <https://drive.google.com/file/d/1XmQ_LO16bQimNSRvnuCzu6Uw35mRz1sx/view?usp=drive_web> params.py <https://drive.google.com/file/d/1I9gZuxjl_T4N8e0pX6GFn-GrAhiJAA4Q/view?usp=drive_web> phy.log <https://drive.google.com/file/d/1XnXZCC4XtEmDaxNFpr-Dtl9tmk_xzz0_/view?usp=drive_web> rez.mat <https://drive.google.com/file/d/11k3b9YuF238gGjhn_0PvDUWOIMU-9N3r/view?usp=drive_web> similar_templates.npy <https://drive.google.com/file/d/1LLJ3UFwDH7OfeHrLMA0Upi6TK-y2r7P7/view?usp=drive_web> spike_clusters.npy <https://drive.google.com/file/d/1JDgeb-A39dJ8VfdFYu__bChWWeEagRAP/view?usp=drive_web> spike_templates.npy <https://drive.google.com/file/d/1DC8ZuVfyEtBy0VGVZ6--rYB-m_dmnMjK/view?usp=drive_web> spike_times.npy <https://drive.google.com/file/d/1JZ7MMVIDZ7jQJw7bb3d8C0FSZ1kFem7n/view?usp=drive_web> templates.npy <https://drive.google.com/file/d/1JZQ1XkkcsbzqxBkOXhbjsnxXCfAPZzoU/view?usp=drive_web> templates_ind.npy <https://drive.google.com/file/d/1nQmFoLNpZPiEOG-EBLdwxOo1jlfMQOwd/view?usp=drive_web> whitening_mat.npy <https://drive.google.com/file/d/10Pdj2LxK5WsSFu1X18GnBCz-YaDBpKZz/view?usp=drive_web> whitening_mat_inv.npy <https://drive.google.com/file/d/1EC3zKVck4JV1X_qh4oWBjGa4zs7xLJem/view?usp=drive_web> On Thu, Jun 2, 2022 at 8:12 AM Olivier Winter ***@***.***> wrote: > Hi, > Yes it is probable since exporting after manual curation is not something > we are super familiar with. > Would you mind sharing the dataset with us so we can reproduce this > locally ? > > If you do not want to post the dataset publicly, you can contact me by > email or at ***@***.*** > > — > Reply to this email directly, view it on GitHub > <#308 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ARV7RIU5TK7GCU4UKIO7KGTVNBND7ANCNFSM5WI7F6YA> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- *_____* *Antara Majumdar* DPhil Physiology, Anatomy and Genetics | Kellogg College University of Oxford | Lak Lab Department of Physiology, Anatomy and Genetics Sherrington Building, Sherrington Rd, Oxford OX1 3PT Tel: +44 07709252462

-- *_____* *Antara Majumdar* DPhil Physiology, Anatomy and Genetics | Kellogg College University of Oxford | Lak Lab Department of Physiology, Anatomy and Genetics Sherrington Building, Sherrington Rd, Oxford OX1 3PT Tel: +44 07709252462

Author

antaramaj16 commented Jun 3, 2022

Here is a folder with the dataset in case it is hard to access this: https://drive.google.com/drive/folders/15fkZI244jwedu6KOB5krK1qu8D02Opz5?usp=sharing

micheleangelofabbri assigned oliche

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