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Using micro_sam on BAND

BAND is a service offered by EMBL Heidelberg that gives access to a virtual desktop for image analysis tasks. It is free to use and micro_sam is installed there. In order to use BAND and start micro_sam on it follow these steps:

Start BAND

  • Go to https://band.embl.de/ and click Login. If you have not used BAND before you will need to register for BAND. Currently you can only sign up via a Google account.
  • Launch a BAND desktop with sufficient resources. It's particularly important to select a GPU. The settings from the image below are a good choice.
  • Go to the desktop by clicking GO TO DESKTOP in the Running Desktops menu. See also the screenshot below.

image

Start micro_sam in BAND

  • Select Applications -> Image Analysis -> uSAM (see screenshot) image
  • This will open the micro_sam menu, where you can select the tool you want to use (see screenshot). Note: this may take a few minutes. image
  • For testing if the tool works, it's best to use the 2d annotator first.
    • You can find an example image to use here: /scratch/cajal-connectomics/hela-2d-image.png. Select it via Select image. (see screenshot) image
  • Then press 2d annotator and the tool will start.

Transfering data to BAND

To copy data to and from BAND you can use any cloud storage, e.g. ownCloud, dropbox or google drive. For this, it's important to note that copy and paste, which you may need for accessing links on BAND, works a bit different in BAND:

  • To copy text into BAND you first need to copy it on your computer (e.g. via selecting it + Ctrl + C).
  • Then go to the browser window with BAND and press Ctrl + Shift + Alt. This will open a side window where you can paste your text via Ctrl + V.
  • Then select the text in this window and copy it via Ctrl + C.
  • Now you can close the side window via Ctrl + Shift + Alt and paste the text in band via Ctrl + V

The video below shows how to copy over a link from owncloud and then download the data on BAND using copy and paste:

simplescreenrecorder-2023-10-16_20.11.42.mp4