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fish-quant / fq-imjoy

ImJoy plugins to run different smFISH analysis in a user-friendly setting.
https://fq-imjoy.readthedocs.io/en/latest/
MIT License
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Root folder 'Specified data path does not EXIST. No images found.' #56

Open Noa164 opened 1 year ago

Noa164 commented 1 year ago

Hi, I have a mac, and my root folder is '/Users/noni/Library/CloudStorage/OneDrive-weizmann.ac.il/1st Rotation/FISHquant/results', somehow it doesn't seem to find it, I feel like I missed something obvious. thanks!

cynthiamoncadareid commented 1 year ago

Hi, I have a mac, and my root folder is '/Users/noni/Library/CloudStorage/OneDrive-weizmann.ac.il/1st Rotation/FISHquant/results', somehow it doesn't seem to find it, I feel like I missed something obvious. thanks!

Hi, I'm having a similar problem where no matches are found even though the regular expression of my files and location are correct. Were you able to figure this out?

Noa164 commented 1 year ago

Unfourtuntely no.

קבל ‏Outlook עבור Android‏https://aka.ms/AAb9ysg

From: Cynthia Moncada-Reid @.> Sent: Monday, January 30, 2023 7:18:28 PM To: fish-quant/fq-imjoy @.> Cc: Noa Frydman @.>; Author @.> Subject: Re: [fish-quant/fq-imjoy] Root folder 'Specified data path does not EXIST. No images found.' (Issue #56)

Hi, I have a mac, and my root folder is '/Users/noni/Library/CloudStorage/OneDrive-weizmann.ac.il/1st Rotation/FISHquant/results', somehow it doesn't seem to find it, I feel like I missed something obvious. thanks!

Hi, I'm having a similar problem where no matches are found even though the regular expression of my files and location are correct. Were you able to figure this out?

— Reply to this email directly, view it on GitHubhttps://github.com/fish-quant/fq-imjoy/issues/56#issuecomment-1409013284, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUZTLHKTQTV7K2MIIEE7UFLWU7ZWJANCNFSM6AAAAAATNRYYAQ. You are receiving this because you authored the thread.Message ID: @.***>

muellerflorian commented 1 year ago

Hello, sorry for the long silence.

Could you post a detailed error message (or send it to me directly by mail, muellerf.research@gmail.com)

see https://fq-imjoy.readthedocs.io/en/latest/contact/#reporting-bugs for how to get these error messages.

I will try to have a look for how to fix this asap.

best F

muellerflorian commented 1 year ago

Hello, after some direct discussion with cynmoncadareid, we identified what was the issue in her case. In short, the definition of th channels was not set correctly.

=====

image

the script will then go over all files in the folder and only use the ones that have 647cmaf as a channel identifier.

In principle, you can add multiple channels, and only images where all of these channels are present will be considered. but after that, you will only be able to process each channel separately. so this option is actually not extremely useful and might be removed in the future

muellerflorian commented 1 year ago

@Noa164 , do you think your issue might be related to that? If not, could you send me some screenshots from the error logs?

muellerf.research@gmail.com

see https://fq-imjoy.readthedocs.io/en/latest/contact/#reporting-bugs for how to get these error messages.

Noa164 commented 1 year ago

the input

image

the error message

image

the files

image
muellerflorian commented 1 year ago

Hello @Noa164 ,

the problem is that on the demo version on the web, you can't access your local folder since the computation is done on a remote server.

if you want to use your own data, you have two choices

  1. You install a local version of ImJoy with FISH-quant as described in the user manual
  2. You provide your test data as a zip archive (following the same organization as the provided test data) and use that it in the demo version. this is really only for testing since larger analysis can't really be done.

hope this helps