- Created by Nicolas Stifani, last modified on Aug 01, 2021
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HP Z840 Deconvolution and Image Analysis Workstation
Roger Gaudry R-619
Applications
2D and 3D Deconvolution
Image processing
Image Analysis
Quantification
Processor
2 x Intel Xeon E5-2623 v4 2.60 GHz
RAM
128 GB (8x16GB) ECC DDR4 2400 MHz
Drives
- 512 GB NVMe at 2500 MB/s OS
- 4 TB (2x2TB) at 170 MB/s spanned volume for storage
Video Card
NVidia GTX 1080 with 8GB DDR5 dedicated memory
Monitor
HP Z24n 24" IPS display native resolution 1920 x 1200
- OS
- Windows 10 21H1
- Softwares
ImageJ
FIJI
Microsoft Office 2016
NIS-Elements AR v5.02 64-bits
NIS Elements Offline Deconvolution v4.11 64-bits
- Turn on the computer
- Log in Windows using your UdM credentials
- Start-up NIS-Elements Offline Deconvolution
- Save your data
- Close NIS-Elements
- Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
- Files can be saved temporarily (during acquisition) on the local C: drive (desktop)
- At the end of each session, copy your data to your external drive and delete it from the local C: drive
- You can store your files on the D: drive (Data Storage). If you do, please create a folder per laboratory using the principal investigator last name. Within, create one folder per user (Firstname_Lastname).
In any case, your files should be removed from the C: drive.
Manuals
- Bring a network cable to connect directly to Ti2 microscope workstation
- Windows 10 UdeM Image installation
- Change the 2nd network adapter configuration with fix IP to enable for computer to computer communication
- Change sharing policies of public document folder
Stand
- Nikon Eclipse E600 upright Serial 725540
Light sources
- Transmitted light Halogen 12V 100W Serial 01875599
- Reflected light
- Power supply Nikon Mercury lamp Type C SHG1 Serial D12139
- Bulb housing model LH M100C-1 Serial 039326
Condenser
- Condenser Universal C-CU Serial 081901
- Lens Dry NA 0.9
- Filters: Empty, Ph1, Ph2, Ph3, DICM, DICH, Empty
Objectives
- 10x/0.3 Plan Fluor Ph1 DLL WD 16 Air
- 40x/0.75 Plan Fluor Ph2 DLL WD 0.72 Air with PF40 Wollaston prism
- 100x/1.3 Plan Fluor Ph3 DLL WD 0.2 Oil with PF/PA 100 Oil Wollaston prism
- Empty
- Empty
- Empty
Position | Name | Brand | ID | Magnification | Numerical Aperture | Immersion | Type | Working distance (mm) | Transmittance (% [nm]) | Technique | Cover glass thickness (mm) |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 10x/0.3 Air | Nikon | 10x/0.3 Air Plan Fluor Ph1 DLL | 10x | 0.3 | Air | Plan Fluor | 16 | >75% [400-800] | BF, Pol, PhC, Fluo | 0.17 |
2 | 40x/0.75 Air | Nikon | 40x/0.75 Air Plan Fluor Ph2 DLL | 40x | 0.75 | Air | Plan Fluor | 0.72 | >80% [400-750] | BF, Pol, PhC, Fluo | 0.17 |
3 | 100x/1.3 Oil | Nikon | 100x/1.3 Oil Plan Fluor Ph3 DLL | 100x | 1.3 | Oil | Plan Fluor | 0.2 | >75% [400-800] | BF, Pol, PhC, Fluo | 0.17 |
4 | Empty | ||||||||||
5 | Empty | ||||||||||
6 | Empty |
Filters
DAPI/Hoechst/AMCA
FITC/EGFP
TRITC/Rhodamine
TexasRed
Position | Cube name | Brand | ID | Excitation Filter | Dichroic mirror | Emission Filter |
---|---|---|---|---|---|---|
1 | DAPI/Hoechst/AMCA | Chroma | Cube set 31000v2 | 350/50x [325-375] | 400LP | 460/50m [435-485] |
2 | FITC/EGFP | Chroma | Cube set 41001 | 480/40x [420-500] | 535/50m [510-560] | |
3 | TRITC/Rhodamine | Chroma | 545/30x [530-560] | 570LP | 620/60m [590-650] | |
4 | Texas Red | Chroma | 560/55x [532-588] | 595LP | 645/75m [607-682] | |
5 | Empty | |||||
6 | Empty |
Detector
- Color Camera Nikon DS-Ri2 Serial 701234
Workstation
- HP Z440 Workstation
- Intel Xeon E5-1630 v3 @ 3.7GHz
- RAM 32 GB DDR4 2133 MHz (4 x 8 GB)
- OS 256GB SSD 550 MBs
- 2TB HD Data Storage 150 MBs
- Video Card NVIDIA Quadro K620 2 GB DDR3 dedicated memory
- Monitor HP Z24i display 24' 1920x1200
Consumables
- Mercury lamp bulb OSRAM HBO 1003W/2 100W
- Tungsten Halogen Lamp OSRAM 64623 HLX 100W 12V
Deconvolution processing not giving expected results...
This usually happens when the image files do not contain the correct metadata.
- Make sure to save the files with all available metadata on the microscope used for the acquisition.
This usually requires to save the files in the software propriatery format (.nd for NIS-Elements and Metamorph, .czi for Zen,...) - You can always add the correct calibration values after acquisition (pixel size in XY and Z, wavelength, Z-step)
Can I use this workstation remotely?
- Yes and No. You can't use the software remotely but you can start the software locally and connect remotely to make sure all is running smoothly. To do so you need to request permission to the platform manager.
Which deconvolution method should I use?
- There is not a single answer
- If you have a single plan you should choose 2D deconvolution. If you have a Z-stack you should pick 3D deconvolution.
- If you want to have a quick view of the result you should use Fast Deconvolution.
- For best results Landweber deconvolution
- For more Yes and No. You can't use the software remotely but you can start the software locally and connect remotely to make sure all is running smoothly. To do so you need to request permission to the platform manager.
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