Closed PathfinderP closed 6 years ago
PathfinderP
commented
6 years ago started <<<< ACCEPT version: 1.0.0-beta 15:43:59: >>>> Session stopped <<<< Output argument "sampleNames" (and maybe others) not assigned during call to "IO.available_samples".
Error in SampleList/updated_input_path (line 124)
Error in SampleList/set.inputPath (line 67)
Error in gui_main (line 45)
Error in ACCEPT (line 44)
MATLAB:unassignedOutputs Error writing to output stream. iostream stream error
LeonieZ
commented
6 years ago Hi,
It seems that in the folder which was saved as the last input folder you chose no samples can be found. If you browse to “C:\Users\user_name\AppData\Local\Temp\ user_name \mcrCache9.3” (number at the end can be different) and search for a file called “LatestSettings.mat” and delete it will open again. Alternatively you can also delete the whole ACCEPT folder in that file location.
When using it again, make sure to select as input folder, the folder that contains a folder for each sample, not the sample folder itself!
From: PathfinderP [mailto:notifications@github.com] Sent: maandag 12 februari 2018 16:47 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [LeonieZ/ACCEPT] Error (#2)
Hi!
I just installed the ACCEPT but when i double click on it to open the following message appears: Output argument ''sampleNames'' (and maybe others) not assigned during call to ''IO.available.samples''. Error in => ACCEPT.m at line 44.
What should i do to solve the problem?
Thank you in advance! Periklis
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/LeonieZ/ACCEPT/issues/2, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJRHq5BEZxSAY0YFi2KdY0ejzpe1jb92ks5tUF0KgaJpZM4SCYDn.
PathfinderP
commented
6 years ago Hi! Great thanks! it works. when i load the input folder, it asks me for manual channel entry. Should i tell the channels and wavelengths of the protocol i used or i just close that window?
Thank you again
Katopodis Periklis
HNZW146, Heinz Wolff Building Institute of Environment, Health and Societies Department of Life Sciences Brunel University London, UK
LinkedIn https://www.linkedin.com/in/periklis-katopodis-568544ab/
On Tue, Feb 13, 2018 at 10:47 AM, LeonieZ notifications@github.com wrote:
Hi,
It seems that in the folder which was saved as the last input folder you chose no samples can be found. If you browse to “C:\Users\user_name\AppData\Local\Temp\ user_name \mcrCache9.3” (number at the end can be different) and search for a file called “LatestSettings.mat” and delete it will open again. Alternatively you can also delete the whole ACCEPT folder in that file location.
When using it again, make sure to select as input folder, the folder that contains a folder for each sample, not the sample folder itself!
From: PathfinderP [mailto:notifications@github.com] Sent: maandag 12 februari 2018 16:47 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [LeonieZ/ACCEPT] Error (#2)
Hi!
I just installed the ACCEPT but when i double click on it to open the following message appears: Output argument ''sampleNames'' (and maybe others) not assigned during call to ''IO.available.samples''. Error in => ACCEPT.m at line 44.
What should i do to solve the problem?
Thank you in advance! Periklis
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ LeonieZ/ACCEPT/issues/2, or mute the threadhttps://github.com/ notifications/unsubscribe-auth/AJRHq5BEZxSAY0YFi2KdY0ejzpe1jb 92ks5tUF0KgaJpZM4SCYDn.
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LeonieZ
commented
6 years ago Hi,
Which sample processor did you choose? If you select the Full Detection it shouldn’t ask you for manual entries. And what kind of sample (from which microscope system) did you use as input?
Leonie
From: PathfinderP [mailto:notifications@github.com] Sent: dinsdag 13 februari 2018 11:58 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com Cc: Zeune, L.L. (TNW) l.l.zeune@utwente.nl; Comment comment@noreply.github.com Subject: Re: [LeonieZ/ACCEPT] Error (#2)
Hi! Great thanks! it works. when i load the input folder, it asks me for manual channel entry. Should i tell the channels and wavelengths of the protocol i used or i just close that window?
Thank you again
Katopodis Periklis
HNZW146, Heinz Wolff Building Institute of Environment, Health and Societies Department of Life Sciences Brunel University London, UK
LinkedIn https://www.linkedin.com/in/periklis-katopodis-568544ab/
On Tue, Feb 13, 2018 at 10:47 AM, LeonieZ notifications@github.com<mailto:notifications@github.com> wrote:
Hi,
It seems that in the folder which was saved as the last input folder you chose no samples can be found. If you browse to “C:\Users\user_name\AppData\Local\Temp\ user_name \mcrCache9.3” (number at the end can be different) and search for a file called “LatestSettings.mat” and delete it will open again. Alternatively you can also delete the whole ACCEPT folder in that file location.
When using it again, make sure to select as input folder, the folder that contains a folder for each sample, not the sample folder itself!
From: PathfinderP [mailto:notifications@github.com] Sent: maandag 12 februari 2018 16:47 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com<mailto:ACCEPT@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: [LeonieZ/ACCEPT] Error (#2)
Hi!
I just installed the ACCEPT but when i double click on it to open the following message appears: Output argument ''sampleNames'' (and maybe others) not assigned during call to ''IO.available.samples''. Error in => ACCEPT.m at line 44.
What should i do to solve the problem?
Thank you in advance! Periklis
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ <https://github.com/%0b> LeonieZ/ACCEPT/issues/2>, or mute the threadhttps://github.com/ <https://github.com/%0b> notifications/unsubscribe-auth/AJRHq5BEZxSAY0YFi2KdY0ejzpe1jb 92ks5tUF0KgaJpZM4SCYDn>.
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PathfinderP
commented
6 years ago Dear Leonie,
I am using images from Image Stream exported from AMNIS software in .tiff format. And yes, on full detection it s not asking for manual entry but it s prossesing the images for ever. Maybe can't recognise the tiffs from this software(?)
Thank you for your replies, Periklis
Katopodis Periklis
HNZW146, Heinz Wolff Building Institute of Environment, Health and Societies Department of Life Sciences Brunel University London, UK
LinkedIn https://www.linkedin.com/in/periklis-katopodis-568544ab/
On Thu, Feb 15, 2018 at 8:33 AM, LeonieZ notifications@github.com wrote:
Hi,
Which sample processor did you choose? If you select the Full Detection it shouldn’t ask you for manual entries. And what kind of sample (from which microscope system) did you use as input?
Leonie
From: PathfinderP [mailto:notifications@github.com] Sent: dinsdag 13 februari 2018 11:58 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com Cc: Zeune, L.L. (TNW) l.l.zeune@utwente.nl; Comment < comment@noreply.github.com> Subject: Re: [LeonieZ/ACCEPT] Error (#2)
Hi! Great thanks! it works. when i load the input folder, it asks me for manual channel entry. Should i tell the channels and wavelengths of the protocol i used or i just close that window?
Thank you again
Katopodis Periklis
HNZW146, Heinz Wolff Building Institute of Environment, Health and Societies Department of Life Sciences Brunel University London, UK
LinkedIn https://www.linkedin.com/in/periklis-katopodis-568544ab/
On Tue, Feb 13, 2018 at 10:47 AM, LeonieZ <notifications@github.com< mailto:notifications@github.com>> wrote:
Hi,
It seems that in the folder which was saved as the last input folder you chose no samples can be found. If you browse to “C:\Users\user_name\AppData\Local\Temp\ user_name \mcrCache9.3” (number at the end can be different) and search for a file called “LatestSettings.mat” and delete it will open again. Alternatively you can also delete the whole ACCEPT folder in that file location.
When using it again, make sure to select as input folder, the folder that contains a folder for each sample, not the sample folder itself!
From: PathfinderP [mailto:notifications@github.com] Sent: maandag 12 februari 2018 16:47 To: LeonieZ/ACCEPT <ACCEPT@noreply.github.com<mailto: ACCEPT@noreply.github.com>> Cc: Subscribed <subscribed@noreply.github.com<mailto:subscribed@noreply. github.com>> Subject: [LeonieZ/ACCEPT] Error (#2)
Hi!
I just installed the ACCEPT but when i double click on it to open the following message appears: Output argument ''sampleNames'' (and maybe others) not assigned during call to ''IO.available.samples''. Error in => ACCEPT.m at line 44.
What should i do to solve the problem?
Thank you in advance! Periklis
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ <https://github.com/%0b> LeonieZ/ACCEPT/issues/2>, or mute the thread< https://github.com/ https://github.com/%0b> notifications/unsubscribe-auth/AJRHq5BEZxSAY0YFi2KdY0ejzpe1jb
92ks5tUF0KgaJpZM4SCYDn>.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/LeonieZ/ACCEPT/issues/2#issuecomment-365225777, or mute the thread https://github.com/notifications/unsubscribe-auth/AifkWX93JRjAr4NH9hpj_ 56f6Ys-JEmyks5tUWhagaJpZM4SCYDn .
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LeonieZ
commented
6 years ago Dear Perikli,
In general it should be possible to process your tiff images, but you should copy the file that I attached in your folder and adjust it to your channel names. And the images for all channels should be separate (with the corresponding name of the marker that you fill in the excel file somewhere in the filename, e.g. 001_PE.tif, 001_DAPI.tif, 001_PerCP.tif) and not stitched to one large image. If your scan consists of around 200 images it should take about 20-30 minutes dependent on the amount of cells found.
Leonie
From: PathfinderP [mailto:notifications@github.com] Sent: donderdag 15 februari 2018 11:24 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com Cc: Zeune, L.L. (TNW) l.l.zeune@utwente.nl; Comment comment@noreply.github.com Subject: Re: [LeonieZ/ACCEPT] Error (#2)
Dear Leonie,
I am using images from Image Stream exported from AMNIS software in .tiff format. And yes, on full detection it s not asking for manual entry but it s prossesing the images for ever. Maybe can't recognise the tiffs from this software(?)
Thank you for your replies, Periklis
Katopodis Periklis
HNZW146, Heinz Wolff Building Institute of Environment, Health and Societies Department of Life Sciences Brunel University London, UK
LinkedIn https://www.linkedin.com/in/periklis-katopodis-568544ab/
On Thu, Feb 15, 2018 at 8:33 AM, LeonieZ notifications@github.com<mailto:notifications@github.com> wrote:
Hi,
Which sample processor did you choose? If you select the Full Detection it shouldn’t ask you for manual entries. And what kind of sample (from which microscope system) did you use as input?
Leonie
From: PathfinderP [mailto:notifications@github.com] Sent: dinsdag 13 februari 2018 11:58 To: LeonieZ/ACCEPT ACCEPT@noreply.github.com<mailto:ACCEPT@noreply.github.com> Cc: Zeune, L.L. (TNW) l.l.zeune@utwente.nl<mailto:l.l.zeune@utwente.nl>; Comment < comment@noreply.github.commailto:comment@noreply.github.com> Subject: Re: [LeonieZ/ACCEPT] Error (#2)
Hi! Great thanks! it works. when i load the input folder, it asks me for manual channel entry. Should i tell the channels and wavelengths of the protocol i used or i just close that window?
Thank you again
Katopodis Periklis
HNZW146, Heinz Wolff Building Institute of Environment, Health and Societies Department of Life Sciences Brunel University London, UK
LinkedIn https://www.linkedin.com/in/periklis-katopodis-568544ab/
On Tue, Feb 13, 2018 at 10:47 AM, LeonieZ <notifications@github.com< mailto:notifications@github.com%3c%0b> mailto:notifications@github.com>> wrote:
Hi,
It seems that in the folder which was saved as the last input folder you chose no samples can be found. If you browse to “C:\Users\user_name\AppData\Local\Temp\ user_name \mcrCache9.3” (number at the end can be different) and search for a file called “LatestSettings.mat” and delete it will open again. Alternatively you can also delete the whole ACCEPT folder in that file location.
When using it again, make sure to select as input folder, the folder that contains a folder for each sample, not the sample folder itself!
From: PathfinderP [mailto:notifications@github.com] Sent: maandag 12 februari 2018 16:47 To: LeonieZ/ACCEPT <ACCEPT@noreply.github.com<mailto: mailto:ACCEPT@noreply.github.com%3cmailto:%0b> ACCEPT@noreply.github.commailto:ACCEPT@noreply.github.com>> Cc: Subscribed <subscribed@noreply.github.com<mailto:subscribed@noreply. mailto:subscribed@noreply.github.com%3cmailto:subscribed@noreply.%0b> github.com>> Subject: [LeonieZ/ACCEPT] Error (#2)
Hi!
I just installed the ACCEPT but when i double click on it to open the following message appears: Output argument ''sampleNames'' (and maybe others) not assigned during call to ''IO.available.samples''. Error in => ACCEPT.m at line 44.
What should i do to solve the problem?
Thank you in advance! Periklis
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ <https://github.com/%0b> https://github.com/%0b> LeonieZ/ACCEPT/issues/2>, or mute the thread< https://github.com/ https://github.com/%0b> notifications/unsubscribe-auth/AJRHq5BEZxSAY0YFi2KdY0ejzpe1jb
92ks5tUF0KgaJpZM4SCYDn>.
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1006478712
commented
6 years ago Dear Leonie,
I am using images from Image Stream exported from EVOS FL 2 in .tiff format. However when I use ACCEPT, it is prossesing the images for ever. What is the required image format?
Thank you for your replies, Yi Wang
LeonieZ
commented
6 years ago Dear Yi Wang,
probably it is also not recognizing your channel names correctly, take the attached document, adjust it to your channel names and save it as .csv in the folder with all your images. And as I said above, the images should not be stitched to one large image covering the full surface recorded.
Hi!
I just installed the ACCEPT but when i double click on it to open the following message appears: Output argument ''sampleNames'' (and maybe others) not assigned during call to ''IO.available.samples''. Error in => ACCEPT.m at line 44.
What should i do to solve the problem?
Thank you in advance! Periklis