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 ~]# docker --version
Docker version 29.1.5, build 0e6fee6
 
[root@rockylinux9 ~]# mkdir /apps/SmartScope/src -p
[root@rockylinux9 ~]# cd /apps/SmartScope/src
[root@rockylinux9 src]# wget docs.smartscope.org/downloads/SmartScopeInstallation.tar.gz --no-check-certificate
 
[root@rockylinux9 src]# cd ..
[root@rockylinux9 SmartScope]# tar xf src/SmartScopeInstallation.tar.gz
[root@rockylinux9 SmartScope]# chown -R root:root ./*
[root@rockylinux9 SmartScope]# ls -l
total 20
-rw-rw-r--. 1 root root  191 Sep  1  2023 database.conf
-rw-rw-r--. 1 root root 1900 Sep  1  2023 docker-compose.yml
drwxrwxr-x. 2 root root   27 Aug 29  2023 shared
-rw-rw-r--. 1 root root  852 Aug 29  2023 smartscope.conf
-rw-rw-r--. 1 root root 1480 Sep  1  2023 smartscope.sh
-rw-rw-r--. 1 root root  593 Aug 29  2023 smartscope.yml
drwxr-xr-x. 2 root root   43 Jan 26 11:29 src
 
[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
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]#

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 ##########
      - ./data:/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/
      # Example:
      # - /mnt/gatan_Raid_X/smartscope/:/mnt/arctica/

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/

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

[root@rockylinux9 SmartScope]# ./smartscope.sh start
 :
 :
[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 stop
[root@rockylinux9 SmartScope]# ./smartscope.sh start

[root@rockylinux9 SmartScope]# ./smartscope.sh start
[root@rockylinux9 SmartScope]# docker ps
CONTAINER ID   IMAGE                            COMMAND                  CREATED          STATUS                         PORTS      NAMES
b6a90b7648ed   nginx                            "/docker-entrypoint.…"   12 seconds ago   Restarting (1) 3 seconds ago              smartscope-nginx-1
9ae9d90650c5   ghcr.io/niehs/smartscope:0.9.1   "/opt/smartscope/Doc…"   12 seconds ago   Up 11 seconds                             smartscope
9e537fb1bd80   redis:6.2-alpine                 "docker-entrypoint.s…"   12 seconds ago   Up 11 seconds                  6379/tcp   smartscope-cache-1
227826eb5e3d   mariadb:10.5                     "docker-entrypoint.s…"   12 seconds ago   Up 11 seconds                  3306/tcp   smartscope-db
 
[root@rockylinux9 SmartScope]#
[root@rockylinux9 SmartScope]# vi shared/nginx/default.conf
 :
server {
        listen 80;
        # listen [::]:80;    <--- 先頭に[#]を入れて無効化します
        server_name _;
 :
[root@rockylinux9 SmartScope]#
[root@rockylinux9 SmartScope]# docker rm -f smartscope-nginx-1
 
[root@rockylinux9 SmartScope]# ./smartscope.sh start
 
[root@rockylinux9 SmartScope]# docker ps
CONTAINER ID   IMAGE                            COMMAND                  CREATED         STATUS         PORTS                   NAMES
275a668b1ad2   nginx                            "/docker-entrypoint.…"   6 minutes ago   Up 6 minutes   0.0.0.0:48000->80/tcp   smartscope-nginx-1
9bff20171252   ghcr.io/niehs/smartscope:0.9.1   "/opt/smartscope/Doc…"   7 minutes ago   Up 7 minutes                           smartscope
ac405a11ec55   redis:6.2-alpine                 "docker-entrypoint.s…"   7 minutes ago   Up 7 minutes   6379/tcp                smartscope-cache-1
2f7d9eab9a5f   mariadb:10.5                     "docker-entrypoint.s…"   7 minutes ago   Up 7 minutes   3306/tcp                smartscope-db
 
[root@rockylinux9 SmartScope]#　
[root@rockylinux9 SmartScope]# lsof -i -P
 :
docker-pr 22302   root    7u  IPv4 140958      0t0  TCP *:48000 (LISTEN)
 :
[root@rockylinux9 SmartScope]#