Root folder 'Specified data path does not EXIST. No images found.'

[Noa164]

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!

[cynmoncada]

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]

Unfourtuntely no. קבל ‏Outlook עבור Android‏<https://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 GitHub<#56 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUZTLHKTQTV7K2MIIEE7UFLWU7ZWJANCNFSM6AAAAAATNRYYAQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[muellerflorian]

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]

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.

=====

• for a file-name hcr3animal1_q4mid_647cmaf.tif, the channel is 647cmaf
• to analyze all images of this channel, in the GUI the following has to be specified

- a name: you can use whatever you want, e.g. fish-1
- for the identifier, you will need to specify exactly what the regular expression will extract from the file-name, e.g. 647cmaf
- no need to add more channels (see below)

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]

@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]

the input

the error message

the files

[muellerflorian]

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