Image Analysis
Image analysis software
CSIF provides several licensed software, such as Huygens Pro , Imaris, Microvolution, SPCImage, ZEN, Leica LAS X, keyed-Metamorph, Matlab, Fiji, Cellpose, CellProfiler, CellProfiler-Analyst, Trackmate, QuPath, Napari, NVivo, ChimeraX , 3dMod/IMOD or Adobe Creative Cloud Apps, Volocity 6.3, for image analysis on our workstations available for local and remote access.
Workstations available within the CSIF:
In Beckman, Room B050, available for remote access:
- WS1 aka “csif-7910” (remote/in-person): csif-7910 (Imaris, Volocity, Zen blue, Cellpose2, Fiji, Napari, Matlab, LAS X, NVivo)
- CPU: 2 Xeon E5-2650 v3 @ 2.30GHz, 25MB (20 Cores)
- RAM: 128G, 16X8G, 2133Mhz
- GPU: 12 GB NVIDIA Quadro M6000
- WS2 aka "csif-dive-ws" (remote/in-person): csif-dive-ws (Las-x, Imaris, Fiji, Cellpose2, CellProfiler, CellProfiler-Analyst, Trackmate, QuPath, Napari, ChimeraX, 3dmod/IMOD)
- CPU: Intel Xeon Gold 6244 CPU @3.60GHz
- RAM: 192 GB
- GPU: 24.5GB GDDR6 Quadro RTX6000
- WS3 aka “csif-spcimage”: csif-spcimage(remote/in-person) (Microvolution, Zen black 2.3/zen blue 2.6, Huygens, Matlab, Imaris, CellProfiler4, CellProfiler-Analyst, Trackmate, Cellpose2, QuPath, Napari, NVivo, ChimeraX, Adobe Creative Cloud Apps)
- CPU: 2 Xeon W2125 @ 4GHz (4 Cores)
- RAM: 32G
- GPU: 8GB GDDR5 NVIDIA Quadro P4000
- WS4 aka CSIF-LLS-analysis (remote/in-person)(Microvolution, 3i LLS processing, CellProfiler4, Cellpose2, QuPath, Napari, Imaris, ChimeraX, Imod)
- CPU: Xeon Silver 4116 @ 2.1GHz (2 Processors)
- RAM: 512G
- GPU: 24GB GDDR5 NVIDIA Quadro P6000
In Shriram, Room B023:
- “csif-Imaris” (Imaris, Zen blue, Matlab, NVivo)
- CPU: Xeon E5-2643 v2 @ 3.30GHz (4 Cores, HT 8)
- RAM: 64G, 16X4G, 1600MHz DDR3
- GPU: 1GB NVIDIA Quadro 600
Software available within the CSIF
Imaris (Bitplane) 3D Image Analysis Software
Bitplane Imaris is ideal for visualization and analysis of 3D data sets as well as rendering animations.
Free Imaris File Converter available for download upon request. See Imaris Open for plugins
Location: Beckman Center, Room B050 (Remote instructions, please contact kamanl@stanford.edu)
Location: Beckman Center, Room B050 (in-person use and remote access upon request)
ZEN Blue Carl Zeiss software Desk 3.4
Airyscan processing option and batch processing options on csif-7910.
Location: Beckman Center, Room B050 (Remote instructions, please contact kamanl@stanford.edu)
Volocity (PerkinElemer) 3D Image Analysis Software 6.3
Location: Beckman Center, Room B050 (Remote access, contact kamanl@stanford.edu)
SVI Huygens 3D Image Analysis Software
Location: Beckman Center, Room B050 (for Remote instructions, please contact kamanl@stanford.edu)
SoftWoRx and Monet (OMX/Delta Vision)
- Deconvolution
- Structured Illumination Microscopy (SIM)
- Localization super-res microscopy analysis (STORM)
Location: Beckman Center, Room B050 (book time on OMX system to use).
Also Available
MATLAB
Location: Shriram Center, Room B023
ZENPRO
Location Shriram Center, Room B023
Photoshop
Location: Beckman Center, Room B050
FIJI
Download ImageJ and install it.
For use in your own lab, we recommend the use of Fiji, a free software for microscope images. Fiji is just ImageJ pre-packaged with Bio-Formats and other plugins. It also checks for updates automatically.
MICROVOLUTION Deconvolution Software
Real-time GPU-based 3D Deconvolution, multi-GPU enabled with Batch processing capability
More information relating to Microvolution
Location: Beckman Center, Room B050
(Local/Remote access, contact kamanl@stanford.edu)
License available on csif-lls-analysis has full update permission (currently 2022.01):
License available on csif-spcimage fixed version 2019.02:
