Bug in auto-correlogram display

Question

Bug in auto-correlogram display

Closed this issue 5 years ago · 7 comments

Hi,

I really like phy but i encounter some issue when phy show auto-correlogram, sometime it show me some aberrant auto, here 1 auto which is really nice with phy and totally bad if i make the auto myself :

compare to :

there is several case like that an other exemple:

and

And finally a cross corr between 2 cluster from the same neuron :

I run phy kwik-gui with ubuntu 16.04.
here list of package in my env :

cairo 1.14.6 0
click 6.6 py27_0
colorama 0.3.7 py27_0
cycler 0.10.0 py27_0
cython 0.25.2 py27_0
decorator 4.0.10 py27_1
enum34 1.1.6 py27_0
fontconfig 2.12.1 0
freeglut 2.8.1 0
freetype 2.5.5 1
glib 2.50.2 0
h5py 2.6.0 np110py27_1
harfbuzz 0.9.39 1
hdf5 1.8.16 0
ipython_genutils 0.1.0 py27_0
joblib 0.9.4 py27_0
klusta 3.0.16
libffi 3.2.1 1
libgcc 5.2.0 0
libgfortran 3.0.0 1
libiconv 1.14 0
libpng 1.6.27 0
libxml2 2.9.4 0
matplotlib 1.5.1 np110py27_0
mkl 11.3.3 0
mpi4py 2.0.0 py27_2
mpich2 1.4.1p1 0
numpy 1.10.4 py27_2
openssl 1.0.2j 0
pango 1.40.3 0
pcre 8.39 1
phy 1.0.9
phycontrib 1.0.15
pip 10.0.1
pip 9.0.1 py27_1
pixman 0.34.0 0
progressbar2 3.6.1 py27_0 spyking-circus
psutil 5.0.1 py27_0
pycairo 1.10.0 py27_0
pyopengl 3.1.1a1 np110py27_0
pyparsing 2.1.4 py27_0
pyqt 4.11.4 py27_4
python 2.7.13 0
python-dateutil 2.6.0 py27_0
pytz 2016.10 py27_0
qt 4.8.7 4
readline 6.2 2
scikit-learn 0.17.1 np110py27_2
scipy 0.17.1 np110py27_1
setuptools 27.2.0 py27_0
sip 4.18 py27_0
six 1.10.0 py27_0
spyking-circus 0.5.6 py27_0 spyking-circus
sqlite 3.13.0 0
tk 8.5.18 0
tqdm 4.10.0
tqdm 4.11.2 py27_0
traitlets 4.3.1 py27_0
vispy 0.4.0.106.gf8a69d0 np110py27_0
wheel 0.29.0 py27_0
zlib 1.2.8 3

Any idea?

Answer 1 · 2018-05-16T08:53:06.000Z

one other example, look at auto of cluster n°406, it change when i add 1 more cluster to the cross corr matrix

add 1 cluster :

Answer 2 · 2018-05-16T09:26:25.000Z

I think this is a bug we had before, which was - iirc - due to the way in which phy was subselecting a number of spikes to use for these computations, when the total number of spikes in the cluster is large. I think we fixed it - could you check that you are using the latest version of phy? (follow the instructions to get the "development" version here, at the bottom: https://github.com/kwikteam/phy). You can also try directly increasing the number of spikes used in the computation to test whether this solves it, by changing the number here: https://github.com/kwikteam/phy-contrib/blob/master/phycontrib/kwik/gui.py#L396 (e.g. increase by 100x) @rossant do you know whether the fix we made for the ccgs in templategui was also made to the kwikgui? It looks like their ccg code is a bit different, which seems surprising.

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On Wed, May 16, 2018 at 9:53 AM, llobetv ***@***.***> wrote: one other example, look at auto of cluster n°406, it change when i add 1 more cluster to the cross corr matrix [image: image] <https://user-images.githubusercontent.com/22896067/40106830-56a827f6-58e6-11e8-8339-355ab6b8b10c.png> add 1 cluster : [image: image] <https://user-images.githubusercontent.com/22896067/40106844-5f29fd00-58e6-11e8-912f-5b02b0926404.png> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#149 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHPUP3eoMOM6jYi04JiSYtMzO6DIDtvYks5ty-jygaJpZM4T_6S1> .

Answer 3 · 2018-05-16T10:01:38.000Z

i already install developmental version:
phy 1.0.9
phycontrib 1.0.15

Increasing number of spike for works seems to solve the issue, thanks !

Answer 4 · 2018-05-16T12:16:36.000Z

Great so @rossant the bug is that the updated (fixed) acg/ccg code from template-gui needs to be in kwik-gui too.

Answer 5 · 2019-03-13T11:05:55.000Z

Hi Nick,

in the message from the 16th May 2018 you suggest changing the number of spikes used for the computation of the autocorrelogram.

Do you know where I can find that file? I found a file with the same name here: C:\Users......\AppData\Local\conda\conda\envs\klusta\Lib\site-packages\phycontrib\kwik_gui but it does not seem to be the same. Even the folder is named differently,

Thanks in advance!

Answer 6 · 2019-03-19T20:06:52.000Z

Could you try making a new environment, and reinstalling fresh there? My best guess is that somehow you're on an old version or something, I'm not sure - @rossant would know better.

Answer 7 · 2019-06-14T12:05:01.000Z

this is likely to be fixed in the dev branch of phy