From 28f0f8c9eee57e0e98d4b25c8686c634a3fc1efa Mon Sep 17 00:00:00 2001 From: Constantin Pape Date: Fri, 13 Oct 2023 18:31:57 +0200 Subject: [PATCH] Create band.md --- doc/band.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 doc/band.md diff --git a/doc/band.md b/doc/band.md new file mode 100644 index 00000000..e670bbcf --- /dev/null +++ b/doc/band.md @@ -0,0 +1,24 @@ +# 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](https://github.com/computational-cell-analytics/micro-sam/assets/4263537/f965fce2-b924-4fc8-871b-f3201e502138) + +**Start micro_sam in BAND** +- Select **Applications->Image Analysis->uSAM** (see screenshot) +![image](https://github.com/computational-cell-analytics/micro-sam/assets/4263537/5daeafb3-119b-4104-8708-aab2960cb21c) +- 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](https://github.com/computational-cell-analytics/micro-sam/assets/4263537/900ce0b9-4cf8-418c-94f1-e99ac7bc0086) +- 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](https://github.com/computational-cell-analytics/micro-sam/assets/4263537/5fbd1c53-2ba1-47d4-ae50-dfab890ac9d3) +- Then press **2d annotator** and the tool will start. + +**Transfering data to BAND** +- TODO