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Kouichi C. Nakamura kouichi-c-nakamura MRC Brain Network Dynamics Unit/University of Oxford UK http://researchmap.jp/kouichi_nakamura/ Kouichi is a postdoctoral neuroscientist working at MRC Brain Network Dynamics Unit, University of Oxford, UK.

kouichi-c-nakamura/copytoImagePlus 2

Assuming you have communication between ImageJ and MATLAB via ImageJ-MATLAB, copytoImagePlus allows you to turn a MATLAB array into ImagePlus object.

kouichi-c-nakamura/ijmshow 2

a wrapper of net.imagej.matlab.ImageJMATLABCommands.show() to support opening a MATLAB array as 5D hyperstack in ImageJ

kouichi-c-nakamura/language-spike2 1

Spike2 language support for Atom.

kouichi-c-nakamura/Zotero-translator-SfN-2016 1

Society for Neuroscience Abstract 2016.js is a web translator for the bibliographic software, Zotero. This will allow you to store abstracts into your Zotero library. This translator works for Society for Neuroscience Abstracts from 2016 onwards.

kouichi-c-nakamura/allenCCF 0

Tools to work with Allen Inst CCF data in matlab

kouichi-c-nakamura/Atom-styles-less-for-MATLAB 0

styles.less file customization for MATLAB language

kouichi-c-nakamura/bio-formats-documentation 0

Bio-Formats documentation

kouichi-c-nakamura/CorrerationCoefficient 0

ImageJ plugin code written in JAVA for Nakamura K, Watakabe A, Hioki H, Fujiyama F, Tanaka Y, Yamamori T, Kaneko T (2007) Transiently increased colocalization of vesicular glutamate transporters 1 and 2 at single axon terminals during postnatal development of mouse neocortex: a quantitative analysis with correlation coefficient. Eur J Neurosci 26:3054–3067, http://doi.org/10.1111/j.1460-9568.2007.05868.x

kouichi-c-nakamura/CSL-Nature-DOI 0

Cytation Style Language (CSL) style for Nature with DOI URL links

kouichi-c-nakamura/CSL-Nature-shorter 0

Based on Nature's numbered style but only the first author is shown and title of paper is omitted.

issue openedcortex-lab/allenCCF

10um/pixel reference atlas

Hi there-

I'm wondering if there is any way to preserve image resolution by avoiding the step of downsampling slice images to 800 x 1400 pixels. I have a group of images that average a resolution of ~0.5 um/pixel and the loss of image quality upon transforming to reference atlas images makes for much data loss in cell activity. Would it be possible to upsample a specific atlas section by 20x once matched with a slice before transforming and overlaying the images?

Thanks

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PR merged cortex-lab/allenCCF

Issue 44#

I think I found the bug, double check it though!

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RobertoDF

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RobertoDF

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Issue 44#

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pshamash

commit sha 66720c0d1f33a182fc2a45d31dafebf2e0569adc

Update Display_Probe_Track.m

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philshams

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Merge pull request #47 from philshams/pr/45 Pr/45

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PR merged cortex-lab/allenCCF

Pr/45

Display probe track update from RobertoDF

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PR opened cortex-lab/allenCCF

Pr/45

Display probe track update from RobertoDF

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issue openedJaneliaSciComp/JRCLUST

Tutorial Error - Confirmation Screen Not Opening

Hello,

I am attempting to do the tutorial. I have a .dat file that is without a .meta and .prb file. However the screen that should appear under the "confirmation" section does not load. I am not sure what I am doing wrong or how to troubleshoot. Thanks!

I am running the machine on Windows 10 with a NVIDIA GeForce 3070 GPU.

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issue commentJaneliaSciComp/JRCLUST

Bug - Error message after GUI re-opening and after splitting clusters

The problem still persists with the new commit. The sites still show up in scrambled positions if one saves the first time it runs the full clustering sequence (jrc full) and opens it again (with jrc manual).

And now there is an additional error we had never encountered before. If we now run the full sequence, then do some merging or splitting, save, close, and then re-open with jrc manual we are getting the following error: "Data found to be in an inconsistent state".

franciscamachado

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PR closed cortex-lab/allenCCF

Issue 44#

I think I found the bug, double check it though!

+14 -1

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1 changed file

RobertoDF

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issue commentcortex-lab/allenCCF

error when using it with mac

This should work on mac. I think it didn't find the file it's trying to load, or the file is corrupted maybe. Do you have annotation_volume_10um_by_index.npy on your computer in a place it can be found?

On Fri, Dec 11, 2020 at 11:56 AM jaeeonlee notifications@github.com wrote:

av = readNPY('annotation_volume_10um_by_index.npy'); % the number at each pixel labels the area, see note below Error using == Matrix dimensions must agree.

Error in readNPYheader (line 31) if ~all(magicString == [147,78,85,77,80,89])

Error in readNPY (line 10) [shape, dataType, fortranOrder, littleEndian, totalHeaderLength, ~] = readNPYheader(filename);

Is this error from running this on mac?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cortex-lab/allenCCF/issues/46, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ5IP2IX3QI4TNXSBPTCGLSUJ2OBANCNFSM4UXFBAMQ .

jel0624

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issue openedcortex-lab/allenCCF

error when using it with mac

av = readNPY('annotation_volume_10um_by_index.npy'); % the number at each pixel labels the area, see note below Error using == Matrix dimensions must agree.

Error in readNPYheader (line 31) if ~all(magicString == [147,78,85,77,80,89])

Error in readNPY (line 10) [shape, dataType, fortranOrder, littleEndian, totalHeaderLength, ~] = readNPYheader(filename);

Is this error from running this on mac?

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issue commentcortex-lab/allenCCF

Increase angle left right in allen_cf_npx

This is great, thanks a lot for your quick modification!

RobertoDF

comment created time in 2 months

issue closedcortex-lab/allenCCF

Increase angle left right in allen_cf_npx

Hi,

While it is possible to change the angle of the probe using "up" and "down" arrow, the "left" and "right" don't work properly. If you change both sequentially the result is quite unpredictable.

closed time in 2 months

RobertoDF

issue commentcortex-lab/allenCCF

Allen CCF - transformation function for ROI list

Hi -- I'll copy the response I sent you over email here: Yes this is possible. Note that in addition to the geometric transformation applied during registration, there is also the downsampling (as you mention) and potentially cropping during the histology processing part of the pipeline. So, these steps would need to be taken into account in your solution. Once you apply the multiplication (due to downsampling) and translation (due to cropping if applicable) to the XY coordinates, then you can apply the geometric transform, yielding your desired output.

This can be done by loading the transform data corresponding to the slice of interest, and using the transform it contains, e.g. load("C:\Drive\Histology\for tutorial\SS096\processed\transformations\mouse_1_slice_1_transform_data") geometric_transform = save_transform.transform transformed_coordinates = transformPointsForward(geometric_transform, X, Y) (note: I haven't tested this code, so you'll have to confirm that this works!)

One alternative solution, mentioned in the wiki (https://github.com/cortex-lab/allenCCF/wiki/7.-Analyze-other-types-of-regions-of-interest-(e.g.-cells)), is to " include the ROI image as an additional channel (or the only channel) in the .tif image that undergoes pre-processing and registration (see Pre-processing histology images and Registering slices to the atlas). In this case, the ROI file will be a channel of the pre-processed and transformed image - e.g. '\processed\transformations\slice_1_transformed.tif'. This is recommended if your ROI detection analysis requires high-resolution images. If you use this method for ROIs marking individual cells, or other sparse, point objects, then uncomment the following line to ensure a one-to-one mapping between ROIs in the original and transformed images: rois = uint8(imregionalmax(rois));".

Let me know if you get either of these to work or if you need more guidance.

hossais2

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issue commentcortex-lab/allenCCF

Increase angle left right in allen_cf_npx

I see that it's probably more intuitive/easier to change the angle by x/y coordinates of the bottom of the trajectory rather than the manipulator angles - I've updated it to do this, try it out and let me know how you like it. @RobertoDF this is the behavior I think you originally expected, you might like it more now.

Note: it converts the angle to still report the same manipulator angles along the top since these are what you need to actually set up your manipulator (angle of manipulator relative to mouse & angle of probe on manipulator)

RobertoDF

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Andy Peters

commit sha 0badae49afdc47917b95860ddb57638643c057bf

allen_ccf_npx: angle cartesian Probe angle changes in allen_ccf_npx used to be spherical/in manipulator angles, switched to cartesian for easier UX

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Alan Liddell

commit sha 94c9c137462f55ca7248d944eec21bf2c8a5cd81

consolidate constructors

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Alan Liddell

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doRecompute on import

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IssuesEvent

issue commentcortex-lab/allenCCF

Increase angle left right in allen_cf_npx

Maybe I'm dimwitted, but I find the probe angles very counterintuitive. I expect that when I start the program I can change the ML angle with left/right and the AP angle with forward/back; instead I first have to rotate the probe to -90/+90 before I get behavior that would even start resemble what I expect. In general I don't see the benefit of being able to change the probe angle without actually changing the probe's angle. I think you guys have built a fantastic tool and I'm very happy that you shared it freely, but it would make me incredibly happy if you would add an option to make the probe angles absolute in cartesian space.

RobertoDF

comment created time in 2 months

issue commentflatironinstitute/mountainsort

Error just after installation using conda

This is probably caused by a too-old version of nodejs.

Magland is right. I ran into the same error when I was trying to deploy mountainsort on another machine when using the conda install method. Installing the mountainlab in the conda virtual environment might cause a nodejs version confusion when you have a newer nodejs version in your system environment while there is also an older version of nodejs in your virtual environment.

Check your nodejs version using node -v when the virtual environment is either activated or deactivated, mine was -6.x and -14.x

To update the nodejs inside the virtual environment, simply use conda update -n YOUR_ENVIRONMENT_NAME nodejs.

Hopefully this will solve your issue.

kimjack0

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Alan Liddell

commit sha 4b7eba27b130aefa1a32a4a823f5a7b7ec78a86f

fix typo

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Vincent

commit sha 41de2564d0fbdcddbd4bc5889af2fd78b4a0295d

Make full use of the .prm file in kilosort import prevents overwriting of prm parameter values by default values fixes renumbering of spike sites when KiloSort returns partial channel map

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Vincent

commit sha fa6e381ae6c1ff7805d687cefcfe07c1850232cc

adds trial file and PSTH parameters during bootstrap if file is present

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Vincent

commit sha 32c08fe1abfc46edbbcc58ae4c88c570e9a4c016

temp solution for saveRes

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Vincent

commit sha ada6b300b02d1ea4e6a54aab4fd2e4d1a6be1a00

path to parameter file

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Vincent

commit sha 74d341a5047a29154ab9ce763de7f465b7b2ba51

Adds comment to kilosort-import saveRes

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Alan Liddell

commit sha f25e589e590345f28863f2ff154f522b896406a4

Merge branch 'master' into master

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Alan Liddell

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resolve merge conflicts

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PR merged JaneliaSciComp/JRCLUST

suggested improvements for kilosort import

also adds option to set trial file during bootstrap

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Alan Liddell

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more tests, some bugfixes

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Pull request review commentJaneliaSciComp/JRCLUST

suggested improvements for kilosort import

 function bootstrap(obj, varargin)         end     end end++function [trialFile,psthTimeLimits] = getTrialFile(workingdir, ask)+    if nargin < 2+        ask = 0;+    end++    trialFile = trialFileInDir(workingdir);++    if ~isempty(trialFile) && ask % found a trial file in working directory; confirm+        dlgAns = questdlg(sprintf('Found trial file ''%s''. Use it?', trialFile));+        if strcmp(dlgAns, 'Yes')+            return;

Good point. I didn't test that bit because I skip dialog pop ups (I set ask to false). Setting psthTimeLimits in the else on line 287 is fine. It's overwritten by the settings in the .meta file anyway. This may be improved later.

vncntprvst

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Pull request review commentJaneliaSciComp/JRCLUST

suggested improvements for kilosort import

 function processArgs(obj)                 obj.hCfg = hCfg_;                 obj.res = res_; -                obj.saveRes();+                obj.saveRes(~obj.args{2});

No, it's perfectly fine. Just put a comment there :^)

vncntprvst

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Pull request review commentJaneliaSciComp/JRCLUST

suggested improvements for kilosort import

 function processArgs(obj)                 obj.hCfg = hCfg_;                 obj.res = res_; -                obj.saveRes();+                obj.saveRes(~obj.args{2});

That's not a satisfying solution of course .... Sorry about that.

vncntprvst

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Pull request review commentJaneliaSciComp/JRCLUST

suggested improvements for kilosort import

 function processArgs(obj)                 obj.hCfg = hCfg_;                 obj.res = res_; -                obj.saveRes();+                obj.saveRes(~obj.args{2});

I'm importing spike sorting results from KiloSort in batches and I need a way to overwrite previous imports. Since I already have the confirm_flag option set to False (in obj.args{2}), the tweak here is to use it to set forceOverwrite to True.

vncntprvst

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Pull request review commentJaneliaSciComp/JRCLUST

suggested improvements for kilosort import

 function processArgs(obj)                 obj.hCfg = hCfg_;                 obj.res = res_; -                obj.saveRes();+                obj.saveRes(~obj.args{2});

This is an ugly tweak, sorry, I should have written that cleaner, but some change is needed here to allow the JRClust user to trigger the forceOverwrite option in saveRes when calling 'import-ksort'.

vncntprvst

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