Unable to Read Subfolders

[ImageMembrane]

Hello Everyone! Hope all are having a great day, just had a question regarding the stitching plugin.

My issue is based on the file location of the images I'm trying to stich. The software I'm using to take the photos I would like to stitch (micromanager) has two options on how to save said images:

• Save each image as an image stack and all of the image stacks get saved under a single folder.
• Each image is saved as an individual image, however each image is saved in its own subfolder under a general folder.

If I try to stitch the image stacks, only the first image stack is read and repeated to stitch together

If I try to stitch the individual image files in their own subfolders, the plugin won't be able to read any of them because it does not look into the subfolders within the large general folder. In order for the plugin to work right now, I need to pull out all of the images from their individual folders and put them into a new general folder. This would be fine if I were only threading a 2x2 every once in a blue moon. However, I am dealing with larger repetitive stitches that I would like to automate as fast as I can. This current temporary solution wastes a lot of time and a lot of storage space on the PC. I am wondering if there is any way to best automate this process or for the plugin to properly read the subfolders or image stacks?

Thank you and have a wonderful day,
IM