Miniscope path failed to be found

[GarrettBlair]

Describe the issue

While trying to convert a single imaging session from v4 Miniscope via the GUIDE gui, the ndx-miniscope.yaml cannot be found. Came up 8/7/25 at the NWB NYU workshop

Request Failed
namespace file 
'C\Program Files\NWB GUIDE\resources\app\build\flask\nwb-guide\_internal\ndx_miniscope\spec\ndx-miniscope.namespace.yaml' not found

Steps to Reproduce

Open guide, start a test conversion, and choose 'miniscope imaging and video' (multi stream). Error on clicking next. Single stream 'miniscope imaging' and 'miniscope behavior' also yield the same error

Operating System

Windows 11

GUIDE Version

1.0.6 (current available)

Code of Conduct

Yes

Did you confirm this issue was not already reported?

Yes

[GarrettBlair]

Hey @bendichter, just wondering if there's been any notice of this issue yet?

[rly]

Hi @GarrettBlair thanks for the bug report. I have a tentative fix, but just need to test it on a windows machine. I'll do that today and keep you posted.

[GarrettBlair]

Thanks Ryan, appreciate it

[rly]

Hi @GarrettBlair , this issue is now fixed in the latest 1.0.7 release of NWB GUIDE (installation instructions). However, please note that NWB GUIDE does not yet support upload of external videos, which you likely have.

If you're comfortable with using a terminal with Python installed, you can still complete the DANDI upload process yourself on the files you created using the classic command-line approach. If you didn't override the default conversion output folder at the first step of the pipeline, then your NWB files can be found in the home directory of the GUIDE under the 'conversions' subfolder. Here is an example showing how to use the DANDI command line interface to upload NWB files with videos to the sandbox (staging) server: https://about.dandiarchive.org/blog/2022/03/03/external-links-in-nwb-and-dandi/#code-walkthrough (Related: https://github.com/NeurodataWithoutBorders/nwb-guide/issues/608)

Let me or @bendichter know if you have any questions!

[GarrettBlair]

Thanks Ryan, the conversion is working for me now (with a couple caveats).

1. error if no behavior .avis found.
   Most of my recordings didn't use the miniscope software to record behavior, it's recorded in parallel by another program. Is there a way to have the behavior folder be optional?
   
   

2. error if gain metaData gain parameter is 'int'.
   I did have one session with a miniscope and behavior camera, and tried that one. By default it saved the gain as 8 (integer). If I edit the metaData file in the behavior folder, changing the gain param from 8 to "High", then I can proceed with conversion. Is there a way to have it accept string or int (also for the miniscope metaData, gain can be either)?

Let me know if I should start a new issue either here or neuroconv

[rly]

@GarrettBlair

1. Since some sessions have behavior from Miniscope and others don't, I think you'll have to create two conversion pipelines (projects) in GUIDE, one for each setup. For sessions that do not have behavior from Miniscope, when selecting formats, select "Miniscope Imaging". You can combine files from both pipelines into the same directory before uploading to DANDI.

2. What version of miniscope are you using? Did you set the value to 8? Could you share the metadata JSON file? Is the value 8 only for the behavior metadata JSON or also for the miniscope metadata JSON? It seems like Miniscope v4 accepts only the values "Low", "Medium", and "High" for gain for the miniscope device: https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software/blob/0fecb97cca82c694b1b40dde03cd759e23ad3224/deviceConfigs/userConfigProps.json#L236-L239