Ecosyste.ms: Issues

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GitHub / MouseLand/Kilosort issues and pull requests

#769 - Extracting Cluster Spiketimes

Issue - State: closed - Opened by AidanFishenden 5 months ago - 8 comments

#768 - Confirming Proper Use

Issue - State: closed - Opened by AidanFishenden 6 months ago - 2 comments

#767 - Slow running speed

Issue - State: closed - Opened by Tingchen-G 6 months ago - 13 comments

#766 - BUG: <Crash of Kilosort and/or computer during first clustering>

Issue - State: closed - Opened by ttmysd70c6f5 6 months ago - 21 comments

#764 - GPU question

Issue - State: closed - Opened by HWWiggins 6 months ago - 1 comment

#763 - Creating a tuning curve using spike cluster and spike time data

Issue - State: closed - Opened by AidanFishenden 6 months ago - 2 comments

#762 - BUG: Kilosort3 Phy output has a wrong map if chanMap is not the default value

Issue - State: closed - Opened by Jialiang-Lu 6 months ago - 2 comments
Labels: Kilosort3

#761 - Update basic_example.ipynb

Pull Request - State: closed - Opened by zhang3xing1 6 months ago

#760 - How to increase spike window size

Issue - State: closed - Opened by 1HosseinHeydari8 6 months ago - 1 comment

#759 - QUESTION: Does KS4 implement catGT tshift?

Issue - State: closed - Opened by chris-angeloni 6 months ago - 1 comment

#757 - Restrict template detection to individual shank (kilosort 4)

Issue - State: closed - Opened by Daruum 6 months ago - 4 comments

#756 - BUG: <Can't Run The Package>

Issue - State: closed - Opened by nacefguessaymi 6 months ago - 1 comment

#755 - Using Kilosort with HDF5 (.h5) files (from MultiChannelSystem)

Issue - State: closed - Opened by K-Mritunjay 6 months ago - 3 comments

#754 - Update README.md

Pull Request - State: closed - Opened by nacefguessaymi 6 months ago - 3 comments

#753 - template_matching.align_U changing shape of learned templates

Issue - State: closed - Opened by rachelmcassidy 6 months ago - 3 comments

#752 - How to create a single channel map

Issue - State: closed - Opened by AidanFishenden 6 months ago - 9 comments
Labels: bug

#751 - BUG: <Kilosort4 Google Colab Example Data Sorting>

Issue - State: closed - Opened by ajcheng1 6 months ago - 1 comment

#748 - BUG: Getting strange waveforms with KiloSort4 compared to KiloSort2

Issue - State: closed - Opened by MariaShuja 6 months ago - 1 comment

#747 - BUG: CUDA out of memory error with no other software open

Issue - State: closed - Opened by Lathomas42 7 months ago - 1 comment

#746 - BUG: <CUDA out of memory>

Issue - State: closed - Opened by hemant22 7 months ago - 18 comments

#745 - FEATURE: Applying Kilosort to Microwires in Human Hybrid Electrodes

Issue - State: closed - Opened by XiaoyuZeng 7 months ago - 3 comments

#744 - INSTALLATION: Segmentation fault (core dumped) during the initial call

Issue - State: closed - Opened by ekurtgl 7 months ago - 4 comments

#743 - BUG：GPU calling failure when starting first clustering

Issue - State: closed - Opened by Alchemist-Y 7 months ago - 15 comments

#742 - Bimodal amplitude distribution, nt and under-merging

Issue - State: closed - Opened by Tingchen-G 7 months ago - 5 comments

#741 - Jacob/output docs

Pull Request - State: closed - Opened by jacobpennington 7 months ago
Labels: docs

#740 - BUG: CUDNN_STATUS_NOT_SUPPORTED error

Issue - State: closed - Opened by a-zmz 7 months ago - 1 comment

#738 - FEATURE: <Use saved templates from a model recording session to run kilosort on another session>

Issue - State: closed - Opened by mberns-ru 7 months ago - 1 comment
Labels: enhancement

#736 - [fix] bug in run_kilosort function

Pull Request - State: closed - Opened by jd730 7 months ago

#735 - .rhs (intan) converter

Issue - State: closed - Opened by Lorena-J 7 months ago

#734 - BUG: <after splitting in phy the amp is not recomputed>

Issue - State: closed - Opened by zkcsmxz 7 months ago - 2 comments

#733 - BUG: pytorch not recognizing CUDA 12.4/12.5 drivers

Issue - State: closed - Opened by ryan-budde 7 months ago - 4 comments

#730 - Explanation for the output files

Issue - State: closed - Opened by zkcsmxz 7 months ago - 1 comment
Labels: docs

#728 - FEATURE: Upgrade kilosort without reinstalling it?

Issue - State: closed - Opened by NirvikNU 8 months ago - 1 comment

#727 - waveform duration, minimum firing rate and high pass filter cutoff

Issue - State: closed - Opened by dmitriivasilev 8 months ago - 4 comments

#726 - How to save filtered and whitened data from command prompt?

Issue - State: closed - Opened by hiroyukioya 8 months ago - 2 comments

#725 - Running Kilosort4 is very slow.

Issue - State: closed - Opened by yyyaaaaaaa 8 months ago - 6 comments

#724 - Kilosort4 runs into Zero Division Error - float division by zero

Issue - State: closed - Opened by Sfrap99 8 months ago - 9 comments

#723 - Sorting a subset of channels (Kilosort4)

Issue - State: closed - Opened by a-savoy 8 months ago - 1 comment

#722 - NumPy 2.0 compatibility

Issue - State: open - Opened by jacobpennington 8 months ago
Labels: enhancement

#721 - pytest --run slow gives urllib.error.HTTPError: HTTP Error 403: Forbidden

Issue - State: closed - Opened by Idavr 8 months ago - 3 comments

#720 - fix for cases in which filename contains string "ap" such as subject id

Pull Request - State: closed - Opened by thejanzimmermann 8 months ago - 1 comment

#718 - After converting the Intan data, the loaded data is empty.

Issue - State: closed - Opened by Fusenheizi 8 months ago - 5 comments

#717 - Question: What does kcoords do in Kilosort 4

Issue - State: closed - Opened by msj220001 8 months ago - 2 comments

#715 - Overflow of timestamps in KS4

Issue - State: closed - Opened by seto0425 8 months ago - 24 comments

#714 - BUG:<kilosort4 API to run the kilosort4: too many values to unpack>

Issue - State: closed - Opened by Alchemist-Y 8 months ago - 2 comments

#713 - Template in Kilosort4 and spikeinterface

Issue - State: closed - Opened by yyyaaaaaaa 8 months ago - 1 comment

#712 - Kilosort spike sorting failed cannot compute length

Issue - State: closed - Opened by AbhiSwamiUConn 8 months ago - 4 comments

#710 - help adjusting parameters to control split/merge decisions

Issue - State: closed - Opened by Selmaan 8 months ago - 5 comments

#709 - Kilosort 4 - compatibility with new generation AI chip architectures

Issue - State: closed - Opened by nperentos 8 months ago - 2 comments

#708 - Sorting channel id to a cluster

Issue - State: closed - Opened by ghattasb 8 months ago - 3 comments

#707 - Kilosort2 vs Kilosort4

Issue - State: closed - Opened by EMerinoM14 8 months ago - 6 comments

#706 - How to adjust parameters to improve sorting results?

Issue - State: closed - Opened by StellaFFF 8 months ago - 2 comments

#705 - <Index in position 1 exceeds array bounds. Error in getClosestChannels2... >

Issue - State: closed - Opened by mtehrani-code 8 months ago - 23 comments
Labels: Kilosort2.5

#704 - Suggestion to avoid oom GPU error

Issue - State: closed - Opened by Kayv-cmb 8 months ago - 24 comments

#703 - BUG: <Large number of contaminated clusters in kilosort v4>

Issue - State: closed - Opened by mikemanookin 8 months ago - 5 comments

#702 - Long processing time, GPU not used, and CUDNN_STATUS_NOT_SUPPORTED error

Issue - State: closed - Opened by cbimbo 8 months ago - 9 comments

#701 - KS4 can't open .json file

Issue - State: closed - Opened by StellaFFF 8 months ago - 4 comments

#700 - Probe and .bin file

Issue - State: closed - Opened by Lorena-J 9 months ago - 2 comments

#699 - NP1 Channel Map Scripts?

Issue - State: closed - Opened by EmmaCondon 9 months ago - 2 comments

#698 - Discontinuous recording

Issue - State: closed - Opened by Shadow7912 9 months ago - 14 comments

#697 - Value of amplitude

Issue - State: closed - Opened by Lorena-J 9 months ago - 6 comments

#696 - Slow performance with low video memory

Issue - State: closed - Opened by Alkohost 9 months ago - 5 comments

#695 - Can KS4 analyze a file with 2 segments recordings?

Issue - State: closed - Opened by StellaFFF 9 months ago - 2 comments

#694 - Sorting with probes with no geometry suggestion request

Issue - State: closed - Opened by ryoiwata 9 months ago - 4 comments

#693 - UX request: replace duplicate_spike_bins with duplicate_spike_ms

Issue - State: closed - Opened by WeissShahaf 9 months ago - 2 comments
Labels: enhancement

#690 - Multi-shank issue - incorrect estimation of x centres

Issue - State: closed - Opened by j-moore94 9 months ago - 4 comments

#689 - Comparison of KS2.5 and KS4 parameters

Issue - State: closed - Opened by Djoels 9 months ago - 2 comments
Labels: Kilosort2.5

#687 - Different spike length at different sample frequency.

Issue - State: closed - Opened by JiaHaoNCKU 9 months ago - 3 comments

#686 - Drift Correction issues with multi-shank probe

Issue - State: open - Opened by Selmaan 9 months ago - 27 comments

#685 - BUG: Parameters ccg_threshold and cluster_pcs don't do anything

Issue - State: closed - Opened by EliseA-UoB 9 months ago - 1 comment

#684 - BUG: noise occupies nearly all the clusters in KS4

Issue - State: closed - Opened by Alchemist-Y 9 months ago - 8 comments

#683 - BUG: IndexError in Phy2

Issue - State: closed - Opened by asheff794 9 months ago - 5 comments

#682 - ##cannot mmap an empty file

Issue - State: closed - Opened by senioralmog93 9 months ago - 5 comments

#680 - FEATURE: <Please write a comprehensive title after the 'FEATURE: ' prefix>

Issue - State: closed - Opened by canfora01 9 months ago - 6 comments
Labels: Kilosort2.5

#679 - Initial Usage Error(s): NumPy array is not writable, 0 spikes extracted

Issue - State: closed - Opened by kipkeller 10 months ago - 8 comments

#678 - 2D MEA Probe creation

Issue - State: closed - Opened by yyyaaaaaaa 10 months ago - 8 comments

#677 - BUG: CUDA out of memory

Issue - State: closed - Opened by adam-hockley 10 months ago - 38 comments

#676 - BUG: dminx not calulated

Issue - State: closed - Opened by adam-hockley 10 months ago - 2 comments

#675 - Kilosort 4 - Algorithm missing fast-spiking units/narrow shaped units

Issue - State: closed - Opened by msj220001 10 months ago - 5 comments

#674 - FEATURE: Support for MacOS M series chips

Issue - State: closed - Opened by tabedzki 10 months ago - 2 comments

#673 - BUG: Spike timing in the first batch is not aligned to original signal

Issue - State: closed - Opened by teristam 10 months ago - 2 comments

#671 - Questions of data from custom electrodes

Issue - State: closed - Opened by dcgggg 10 months ago - 1 comment

#670 - CUDA out of memory during saving to phy

Issue - State: closed - Opened by ananmoran 10 months ago - 10 comments
Labels: enhancement