MONAI Label is a free and open-source platform that facilitates the development of AI-based applications that aim at reducing the time required to annotate 3D medical image datasets. It allows researchers to readily deploy their apps as services, which can be made available to clinicians via their preferred user-interface. Currently, MONAI Label readily supports locally installed (3DSlicer) and web-based (OHIF) frontends, and offers two Active learning strategies to facilitate and speed up the training of segmentation algorithms. MONAI Label allows researchers to make incremental improvements to their labeling apps by making them available to other researchers and clinicians alike.

References:

• Andres Diaz-Pinto, Sachidanand Alle, Alvin Ihsani, Muhammad Asad, Vishwesh Nath, Fernando Pérez-García, Pritesh Mehta, Wenqi Li, Holger R. Roth, Tom Vercauteren, Daguang Xu, Prerna Dogra, Sebastien Ourselin, Andrew Feng, M. Jorge Cardoso
  MONAI Label: A framework for AI-assisted Interactive Labeling of 3D Medical Images
  arXiv:2203.12362 [cs.HC]
Documentation
• MONAILabel Home page
• MONAILabel Github page
Important Notes
• Module Name: MONAILabel (see the modules page for more information)
• Unusual environment variables set
  • MONAILABEL_HOME  installation directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.



Interactive use of MONAILabel requires a graphical X11 connection.
Both NX and MobaXterm work well for Windows users,
while XQuartz works well for Mac users.

[user@biowulf]$ sinteractive  --mem=20g --gres=gpu:k80:1,lscratch:10 -c4 
[user@cn0861 ~]$ module load monailabel 
[+] Loading singularity  3.8.5-1  on cn4206
[+] Loading cuDNN/7.6.5/CUDA-10.2 libraries...
[+] Loading CUDA Toolkit  10.2.89  ...
[+] Loading monailabel  0.4.0rc4

[user@cn0861 ~]$ monailabel -h 
...
monailabel/0.4.0rc4/lib/python3.9/site-packages:/usr/local/Anaconda/envs/py3.9/lib/python3.9/site-packages
usage: monailabel [-h] {start_server,apps,datasets,plugins} ...

positional arguments:
  {start_server,apps,datasets,plugins}
                        sub-command help
    start_server        Start Application Server
    apps                list or download sample apps
    datasets            list or download sample datasets
    plugins             list or download viewer plugins

optional arguments:
  -h, --help            show this help message and exit

[user@cn0861 ~]$ PEGASAS pathway -h 
usage: PEGASAS pathway [-h] [-o OUT_DIR] [-n NUM_INTERVAL] [--plotting]
                       geneExpbySample geneSignatureList groupInfo

required arguments:
  geneExpbySample       A TSV format matrix of gene expression values (FPKM,
                        TPM, etc.) where each row is one sample and each
                        column is one gene.
  geneSignatureList     One or multiple gene signature sets of pathway of
                        interest in the format of 'gmt' (see MSigDB webset).
  groupInfo             A TSV format file provides patient ID and
                        phenotype/disease stage in each row.

optional arguments:
  -h, --help            show this help message and exit
  -o OUT_DIR, --out-dir OUT_DIR
                        Output folder name of the analysis.
  -n NUM_INTERVAL, --num-interval NUM_INTERVAL
                        Number of KS enrichment calculation processes one
                        time.
  --plotting            Making plots to inspect K-S enrichment scores.
[user@cn0861 ~]$ monailabel datasets --download --name Task09_Spleen --output datasets 
Task09_Spleen.tar: 1.50GB [00:49, 32.6MB/s]
2022-06-01 07:56:00,592 - INFO - Downloaded: datasets/Task09_Spleen.tar
2022-06-01 07:56:04,484 - INFO - Verified 'Task09_Spleen.tar', md5: 410d4a301da4e5b2f6f86ec3ddba524e.
2022-06-01 07:56:04,485 - INFO - Writing into directory: /gpfs/gsfs7/users/user/MONAILabel/datasets.
Task09_Spleen is downloaded at: datasets/Task09_Spleen
[user@cn0861 ~]$ monailabel apps --download --name radiology --output apps 
radiology is copied at: /gpfs/gsfs7/users/user/MONAILabel/apps/radiology
[user@cn0861 ~]$ firefox & 
[user@cn0861 ~]$ monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit

Navigate the Firefox to the URL: http://127.0.0.1:8000/

[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226