SmartScope

SmartScope is a framework for automated cryo-electron microscopy (Cryo-EM). The main purpose is to automate specimen screening, document the process, 
and provide a portal for visualization and interaction with the microscope. The software bundles a database, the main imaging workflow and a web user-inteface for easy access. 
To run Smartscope, simply fill the form about which grids to be screened, press start and wait for live results to come in.

SmartScopeは自動クライオ電子顕微鏡（Cryo-EM）用のフレームワークです。主な目的は、試料スクリーニングを自動化し、そのプロセスを文書化することです、 
可視化と顕微鏡とのインタラクションのためのポータルを提供することである。このソフトウェアには、データベース、主なイメージングワークフロー、そして簡単にアクセスできるウェブユーザーインターフェイスがバンドルされています。
Smartscopeを実行するには、どのグリッドをスクリーニングするかフォームに記入し、スタートを押し、ライブ結果が来るのを待つだけです。

[root@rockylinux9 ~]# mkdir /apps/SmartScope -p
[root@rockylinux9 ~]# cd /apps/SmartScope/
[root@rockylinux9 SmartScope]# wget https://raw.githubusercontent.com/NIEHS/SmartScope/stable/Docker/SmartScope/smartscope.sh
 
[root@rockylinux9 SmartScope]# ls -lh smartscope.sh
-rw-r--r--. 1 root root 5.5K Mar 28 05:09 smartscope.sh
 
[root@rockylinux9 SmartScope]# chmod +x ./smartscope.sh
[root@rockylinux9 SmartScope]# ./smartscope.sh
 
Usage: smartscope.sh subcommand [command]
 
Subcommand              DESCRIPTION
==========              ===========
start                   Start SmartScope
stop                    Stop smartscope
restart                 Restart smartscope
setup                   Setup the smartscope directories
update version                 Update smartscope to the specified version. Choices: ['latest','stable'] (default: latest)
run command             Run a smartscope command in the smartscope container
exec command            Run any shell command in the smartscope container
python                  Runs an interactive ipython shell inside the smartscope container
 
[root@rockylinux9 SmartScope]#

[root@rockylinux9 SmartScope]# ./smartscope.sh setup stable
 :
 :
[root@rockylinux9 SmartScope]# ls -lh
total 24K
drwxr-xr-x. 2 root root    6 Mar 28 05:12 backups
drwxr-xr-x. 2 root root    6 Mar 28 05:12 data
-rw-r--r--. 1 root root  219 Mar 28 05:12 database.conf
drwxr-xr-x. 2 root root    6 Mar 28 05:12 db
-rw-r--r--. 1 root root 1.7K Mar 28 05:12 docker-compose.yml
drwxr-xr-x. 2 root root    6 Mar 28 05:12 logs
drwxr-xr-x. 5 root root   70 Mar 28 05:12 shared
-rw-r--r--. 1 root root  905 Mar 28 05:12 smartscope.conf
-rwxr-xr-x. 1 root root 5.5K Mar 28 05:09 smartscope.sh
-rw-r--r--. 1 root root  801 Mar 28 05:12 smartscope.yml
[root@rockylinux9 SmartScope]#

version: "3"
services:
  smartscope:
    # image: ghcr.io/niehs/smartscope:0.8-rc.2  #Change version here
    user: ${UID}:${GID} #This corresponds to the user running the smarscope.sh script
    volumes:
      ######## ADD YOUR MAIN DATA LOCATION ##########
      - /mnt/nas/smartscope/:/mnt/data/
      # Example:
      # - /nfs/data/:/mnt/data/
      ######## ADD YOUR MICROSCOPES #########
      # The synthax from the microscope volumes is as follows:
      # - /path/to/where/serialem/will/write/files/:/mnt/your_scope_name_here/
      - /mnt/serialemComputer/smartscope/:/mnt/myscope1/
      # Example:
      # - /mnt/gatan_Raid_X/smartscope/:/mnt/arctica/
  nginx:
    ports:
      #### BROADCASTED PORT ####
      # Default port is 48000 but this can be changed by any port of your choosing.
      # Note: You need sudo permissions to use port 80
      - 48000:80

[root@rockylinux9 SmartScope]# mkdir /mnt/nas/smartscope/ -p
[root@rockylinux9 SmartScope]# mkdir /mnt/serialemComputer/smartscope/ -p

[root@rockylinux9 SmartScope]# ./smartscope.sh start
Checking for updates to version latest
Error: No such object: ghcr.io/niehs/smartscope:latest
Online sha: 50338c9ec3e991710bc34fdacc38dde0c4341cd57c9e91c2cbdfa91087d94996
Local sha:
A new release is available. Run 'smartscope.sh update latest' to update to the latest version.
Checking for updates to version stable
Error: No such object: ghcr.io/niehs/smartscope:stable
Online sha: bc20216eab2e61ead56533c63783dc3d18597d08bbd692f14428404824aba3ec
Local sha:
A new beta version is available. Run 'smartscope.sh update stable' to update to the new beta version.
./smartscope.sh: line 43: UID: readonly variable
Starting smartscope
 :
[root@rockylinux9 SmartScope]#
 
[root@rockylinux9 SmartScope]# lsof -i -P
 :
docker-pr 4892   root    7u  IPv4  44806      0t0  TCP *:48000 (LISTEN)
docker-pr 4898   root    7u  IPv6  44807      0t0  TCP *:48000 (LISTEN)
[root@rockylinux9 SmartScope]#

[root@rockylinux9 SmartScope]# vi smartscope.conf
ALLOWED_HOSTS=localhost
 ↓
ALLOWED_HOSTS=*
[root@rockylinux9 SmartScope]#

[root@rockylinux9 SmartScope]# ./smartscope.sh restart