Can't find colocalization file

VH-Lab / vhlab-microscopyimageanalysis-matlab

Matlab app for analysis of high density imaging data like that from Array Tomography

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Can't find colocalization file #7

Closed berithi closed 6 years ago

berithi commented 6 years ago

After running at_colocalization_shift overnight (and seeing the progress bar at 8% before leaving) I can't find the result file anywhere... When I came in this morning I found the following errors, not sure what they mean: Error using load File name is empty.

Error in atgui2 (line 273) load(cfile);

Error in atgui2 (line 249) atgui2(name,'command',[name 'ATGUI_DrawCLALines'],'fig',fig,'theinput',theinput);

Error in at_itemeditlist_gui (line 305) feval(ud.drawaction,ud.drawaction_userinputs{:},'theinput',myinput);

Error in at_itemeditlist_gui (line 392) at_itemeditlist_gui(name,'command',[name 'drawaction'],'ud',ud);

Error in callbacknametag (line 14) eval([functionname '(''' name ''',''command'',''' tag ''',varargin{:});']);

Error while evaluating UIControl Callback

Got request to draw CLA.

stevevanhooser commented 6 years ago

Thanks, I have a grant due Friday but will get on this after that!

stevevanhooser commented 6 years ago

Berith - what ROIs were you computing the colocalization of? Anything special about the parameters?

berithi commented 6 years ago

Not that I’m aware off, but I’d have to go back and look. I’ll be in lab tomorrow and will let you know... thanks! Berith

Sent from my iPhone

On Jan 20, 2018, at 15:30, Steve Van Hooser notifications@github.com wrote:

Berith - what ROIs were you computing the colocalization of? Anything special about the parameters?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

stevevanhooser commented 6 years ago

I am computing colocalization between vglut2 and psd-95. I found something non-ideal that slowed the process; I fixed it but am letting it re-do the colocalization analysis to make sure it works. Update in the AM...

Steve

stevevanhooser commented 6 years ago

OK, it ran successfully overnight. Seemed to take about 2 hours. I think I've fixed all the little problems that were slowing the calculation.

You can update to the latest version of both vhlab_mlapp_ArrayTomography and vhlab_mltbx_toolbox and you should be in good shape.

Steve

berithi commented 6 years ago

Great! I'll try to rerun it later today or tomorrow. Thanks, b.

On Sun, Jan 21, 2018 at 8:39 AM, Steve Van Hooser notifications@github.com wrote:

OK, it ran successfully overnight. Seemed to take about 2 hours. I think I've fixed all the little problems that were slowing the calculation.

You can update to the latest version of both vhlab_mlapp_ArrayTomography and vhlab_mltbx_toolbox and you should be in good shape.

Steve

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-359249168, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDMA5IeTwuvKwHpLj1oPDYfSy1Sxdks5tMz4UgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251

stevevanhooser commented 6 years ago

The colocalization file is on our server if you don't want to recompute

berithi commented 6 years ago

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser <notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251

stevevanhooser commented 6 years ago

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi notifications@github.com wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser <notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360518318, or mute the thread https://github.com/notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2KaIks5tOKoZgaJpZM4RR1LI.

berithi commented 6 years ago

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser <notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi notifications@github.com wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360519018, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDLiPBN_wk8JXJgHKBA6pREalRwGaks5tOKqcgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251

stevevanhooser commented 6 years ago

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi notifications@github.com wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser <notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi notifications@github.com wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360519018, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDLiPBN_wk8JXJgHKBA6pREalRwGaks5tOKqcgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360521980, or mute the thread https://github.com/notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUtdHks5tOKzMgaJpZM4RR1LI.

berithi commented 6 years ago

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser notifications@github.com wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi notifications@github.com wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser <notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi notifications@github.com wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360519018, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDLiPBN_wk8JXJgHKBA6pREalRwGaks5tOKqcgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360521980, or mute the thread https://github.com/notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUtdHks5tOKzMgaJpZM4RR1LI.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

stevevanhooser commented 6 years ago

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi notifications@github.com wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser notifications@github.com wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi notifications@github.com wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser <notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi notifications@github.com wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360519018, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDLiPBN_wk8JXJgHKBA6pREalRwGaks5tOKqcgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/issues/7#issuecomment-360521980, or mute the thread https://github.com/notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUtdHks5tOKzMgaJpZM4RR1LI.

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berithi commented 6 years ago

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser <notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi notifications@github.com wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser notifications@github.com wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi notifications@github.com wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi notifications@github.com wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI>.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360519018, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDLiPBN_ wk8JXJgHKBA6pREalRwGaks5tOKqcgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360521980>, or mute the thread https://github.com/ notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUt dHks5tOKzMgaJpZM4RR1LI.

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stevevanhooser commented 6 years ago

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi notifications@github.com wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi notifications@github.com wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi notifications@github.com wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI>.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360519018, or mute the thread https://github.com/notifications/unsubscribe-auth/AeniDLiPBN_ wk8JXJgHKBA6pREalRwGaks5tOKqcgaJpZM4RR1LI .

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berithi commented 6 years ago

That would be great! How can I stop the current process? It's preventing me from doing anything else and I need to process the other sample from this set before sending it to you..

On Thu, Jan 25, 2018 at 2:36 PM, Steve Van Hooser notifications@github.com wrote:

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi notifications@github.com wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi notifications@github.com wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi notifications@github.com wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI>.

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-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360521980>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUt dHks5tOKzMgaJpZM4RR1LI>.

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berithi commented 6 years ago

So I put both directories on the server. The files that I'm colocalizing are in YEL22JAN_1_I_1_analysis: vglut1_algnd_threshold_40000_26_vf_3_1000 with psd_algnd_threshold_30000_26_vf_3_1000 and in YEL221AUG_11_I_1_analysis: vglut1_algnd_threshold_40000_26_volfil_3_1000 with psd_algnd_threshold_30000_26_volfil_3_1000 I'm using the default settings of -2 -1 0 1 2 and 0.33%

Thanks again! Berith

On Thu, Jan 25, 2018 at 2:40 PM, Berith Isaac berithi@gmail.com wrote:

That would be great! How can I stop the current process? It's preventing me from doing anything else and I need to process the other sample from this set before sending it to you..

On Thu, Jan 25, 2018 at 2:36 PM, Steve Van Hooser < notifications@github.com> wrote:

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi notifications@github.com wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi notifications@github.com wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi <notifications@github.com

wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI>.

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-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360521980>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUt dHks5tOKzMgaJpZM4RR1LI>.

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stevevanhooser commented 6 years ago

Running...estimates are about 4 hours and 1.5 hours...

On Jan 25, 2018, at 3:25 PM, berithi notifications@github.com wrote:

So I put both directories on the server. The files that I'm colocalizing are in YEL22JAN_1_I_1_analysis: vglut1_algnd_threshold_40000_26_vf_3_1000 with psd_algnd_threshold_30000_26_vf_3_1000 and in YEL221AUG_11_I_1_analysis: vglut1_algnd_threshold_40000_26_volfil_3_1000 with psd_algnd_threshold_30000_26_volfil_3_1000 I'm using the default settings of -2 -1 0 1 2 and 0.33%

Thanks again! Berith

On Thu, Jan 25, 2018 at 2:40 PM, Berith Isaac berithi@gmail.com wrote:

That would be great! How can I stop the current process? It's preventing me from doing anything else and I need to process the other sample from this set before sending it to you..

On Thu, Jan 25, 2018 at 2:36 PM, Steve Van Hooser < notifications@github.com> wrote:

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi notifications@github.com wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi notifications@github.com wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi <notifications@github.com

wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360518318>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjQRNFaLMRjgXHEaGgnAwbhLH2K aIks5tOKoZgaJpZM4RR1LI>.

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-- Berith Isaac berithi@gmail.com 617-301-0251 <(617)%20301-0251> <(617)%20301-0251> <(617)%20301-0251> — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub < https://github.com/VH-Lab/vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-360521980>, or mute the thread < https://github.com/ notifications/unsubscribe-auth/ABznjYau0aMMu7bu7bF5nv4CMmJvUt dHks5tOKzMgaJpZM4RR1LI>.

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berithi commented 6 years ago

That's less then half the time it took on Smintheus! The shorter one of the two finished after 5.5. hours... I'll need to figure out why it's so slow. In the meantime I set up ROIs for two more datasets, but the CLA's for those are supposed to take 19 hours. Is there any chance you could run those as well? I know Sacha (and I) would really appreciate that! The details are: folder YEL05MAY_12_45_49um_analysis ROIs vglut1_threshold_26_3_3000 and PSD95_threshold_26_vf folder YEL05MAY_11_65_67um_1_analysis ROIs vglut1_threshold_26_vf and psd95_threshold_26_vf Thanks so much! Berith

On Thu, Jan 25, 2018 at 5:11 PM, Steve Van Hooser notifications@github.com wrote:

Running...estimates are about 4 hours and 1.5 hours...

On Jan 25, 2018, at 3:25 PM, berithi notifications@github.com wrote:

So I put both directories on the server. The files that I'm colocalizing are in YEL22JAN_1_I_1_analysis: vglut1_algnd_threshold40000 26_vf_3_1000 with psd_algnd_threshold_30000_26_vf_3_1000 and in YEL221AUG_11_I_1_analysis: vglut1_algnd_threshold40000 26_volfil_3_1000 with psd_algnd_threshold_30000_26_volfil_3_1000 I'm using the default settings of -2 -1 0 1 2 and 0.33%

Thanks again! Berith

On Thu, Jan 25, 2018 at 2:40 PM, Berith Isaac berithi@gmail.com wrote:

That would be great! How can I stop the current process? It's preventing me from doing anything else and I need to process the other sample from this set before sending it to you..

On Thu, Jan 25, 2018 at 2:36 PM, Steve Van Hooser < notifications@github.com> wrote:

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi notifications@github.com wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi <notifications@github.com

wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi < notifications@github.com

wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/ vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe-auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

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stevevanhooser commented 6 years ago

Hi Berith -

YEL05MAY_11_65_67um_1_analysis is already there

YEL05MAY_12_45_49um_analysis is now running, says about 2.5 hours

Best Steve

On Jan 25, 2018, at 9:56 PM, berithi notifications@github.com wrote:

That's less then half the time it took on Smintheus! The shorter one of the two finished after 5.5. hours... I'll need to figure out why it's so slow. In the meantime I set up ROIs for two more datasets, but the CLA's for those are supposed to take 19 hours. Is there any chance you could run those as well? I know Sacha (and I) would really appreciate that! The details are: folder YEL05MAY_12_45_49um_analysis ROIs vglut1_threshold_26_3_3000 and PSD95_threshold_26_vf folder YEL05MAY_11_65_67um_1_analysis ROIs vglut1_threshold_26_vf and psd95_threshold_26_vf Thanks so much! Berith

On Thu, Jan 25, 2018 at 5:11 PM, Steve Van Hooser notifications@github.com wrote:

Running...estimates are about 4 hours and 1.5 hours...

On Jan 25, 2018, at 3:25 PM, berithi notifications@github.com wrote:

So I put both directories on the server. The files that I'm colocalizing are in YEL22JAN_1_I_1_analysis: vglut1_algnd_threshold40000 26_vf_3_1000 with psd_algnd_threshold_30000_26_vf_3_1000 and in YEL221AUG_11_I_1_analysis: vglut1_algnd_threshold40000 26_volfil_3_1000 with psd_algnd_threshold_30000_26_volfil_3_1000 I'm using the default settings of -2 -1 0 1 2 and 0.33%

Thanks again! Berith

On Thu, Jan 25, 2018 at 2:40 PM, Berith Isaac berithi@gmail.com wrote:

That would be great! How can I stop the current process? It's preventing me from doing anything else and I need to process the other sample from this set before sending it to you..

On Thu, Jan 25, 2018 at 2:36 PM, Steve Van Hooser < notifications@github.com> wrote:

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi notifications@github.com wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi <notifications@github.com

wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi < notifications@github.com

wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

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berithi commented 6 years ago

That's great and I'm so glad you ran it as well, because my Matlab crashed just a few minutes ago. I'm not sure if it's code related, but here are the details:

On Fri, Jan 26, 2018 at 9:02 AM, Steve Van Hooser notifications@github.com wrote:

Hi Berith -

YEL05MAY_11_65_67um_1_analysis is already there

YEL05MAY_12_45_49um_analysis is now running, says about 2.5 hours

Best Steve

On Jan 25, 2018, at 9:56 PM, berithi notifications@github.com wrote:

That's less then half the time it took on Smintheus! The shorter one of the two finished after 5.5. hours... I'll need to figure out why it's so slow. In the meantime I set up ROIs for two more datasets, but the CLA's for those are supposed to take 19 hours. Is there any chance you could run those as well? I know Sacha (and I) would really appreciate that! The details are: folder YEL05MAY_12_45_49um_analysis ROIs vglut1_threshold_26_3_3000 and PSD95_threshold_26_vf folder YEL05MAY_11_65_67um_1_analysis ROIs vglut1_threshold_26_vf and psd95_threshold_26_vf Thanks so much! Berith

On Thu, Jan 25, 2018 at 5:11 PM, Steve Van Hooser < notifications@github.com> wrote:

Running...estimates are about 4 hours and 1.5 hours...

On Jan 25, 2018, at 3:25 PM, berithi notifications@github.com wrote:

So I put both directories on the server. The files that I'm colocalizing are in YEL22JAN_1_I_1_analysis: vglut1_algnd_threshold40000 26_vf_3_1000 with psd_algnd_threshold_30000_26_vf_3_1000 and in YEL221AUG_11_I_1_analysis: vglut1_algnd_threshold40000 26_volfil_3_1000 with psd_algnd_threshold_30000_26_volfil_3_1000 I'm using the default settings of -2 -1 0 1 2 and 0.33%

Thanks again! Berith

On Thu, Jan 25, 2018 at 2:40 PM, Berith Isaac berithi@gmail.com wrote:

That would be great! How can I stop the current process? It's preventing me from doing anything else and I need to process the other sample from this set before sending it to you..

On Thu, Jan 25, 2018 at 2:36 PM, Steve Van Hooser < notifications@github.com> wrote:

Easy. If you set up the experiments so that the ROIs are detected, I can run them on my machine or other machines over night to process several experiments in one evening

On Thu, Jan 25, 2018 at 1:52 PM, berithi < notifications@github.com> wrote:

So Sacha would really like to get some numbers back on the colocalization in time for his grant (which is due next week). How complicated would it be for me to run this stuff on a cluster? Thanks :-)

On Thu, Jan 25, 2018 at 11:37 AM, Steve Van Hooser < notifications@github.com

wrote:

It may pause for several minutes between removing the progress bar and writing the file; don't panic, just let it finish!

On Jan 25, 2018, at 11:36 AM, berithi < notifications@github.com

wrote:

Ok. I’ll just have to wait patiently then. It looks like it’ll be running for 9 hours, so I’ll know tomorrow. Thanks!

Sent from my iPhone

On Jan 25, 2018, at 11:34, Steve Van Hooser < notifications@github.com> wrote:

The one you're running will create the file when it finishes

Actually, the overlays for ROIs and CLAs currently clash. Just turn on one for right now, please

Thanks Steve

On Jan 25, 2018, at 11:33 AM, berithi < notifications@github.com

wrote:

Got it- both overlays on ROIs and CLA's need to be clicked! The only thing I'm worried about is that the CLA I'm running didn't create a CLA file?

On Thu, Jan 25, 2018 at 11:23 AM, Steve Van Hooser < notifications@github.com

wrote:

Great that the one thing is running..

When you click on overlay, you should see the ROIs of the first channel you had selected when doing the CLA (I guess I did it, so it is the PSD channel) highlighted in whatever color is listed (it was a blue color for me). Only the ROIs that are "colocalized" are highlighted, the others are not.

Steve

On Jan 25, 2018, at 11:21 AM, berithi < notifications@github.com> wrote:

Hi Steve, So I'm running a test run now, and wondering if it's supposed to create a CLA file right from the start? The progress bar is moving (and is showing 6 hours), so that's good I guess. At the same time trying to figure out how to look at the file you created..? What should I see when I click on overlay? Thanks, Berith

On Sun, Jan 21, 2018 at 11:54 AM, Steve Van Hooser < notifications@github.com

wrote:

The colocalization file is on our server if you don't want to recompute

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/VH-Lab/ vhlab_mlapp_ArrayTomography/ issues/7#issuecomment-359262657, or mute the thread https://github.com/notifications/unsubscribe- auth/ AeniDGgrCX1LBYJWzumwMjRz5Do2dgJgks5tM2vSgaJpZM4RR1LI .

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