Image Analysis and Data Management
Image Analysis
Bio-Imaging Resource Center provides a variety of image analysis resources/training:
- One-on-one user imaging data discussion, where we suggest the best software/method/pipeline for image analysis
- Writing of custom image analysis scripts, pipelines, batch processing
- Regular image analysis seminars and workshops
- Image Analysis User Group meetings
- One-on-one user training
- Helpdesk session, every Wednesday, 3-5pm
In addition, we encourage our users to contact us at the experimental design stage to have a discussion with our team of microscopy and image analysis experts, to ensure that the imaging data acquired will be appropriate for the planned analysis and research questions
Software
We have expertise in a variety of image analysis software/tools, which we use to help analyze our users’ imaging data
Open-source software: ImageJ/Fiji, QuPath, Napari, CellProfiler, Icy
Commercial Software: Imaris, Arivis, Aivia, Huygens, MetaMorph
Machine/Deep Learning frameworks: Weka, ilastik, Labkit StarDist, Cellpose, DeepImageJ, ZeroCostDL4Mic
For more information, please visit our Bio-Image Analysis GitHub page.
Here are the details on the available workstations and software for image processing and analysis.
Data Management
User data is transferred from the microscope acquisition computer to the BIRC server, which is for temporary storage and transfer, not for user data storage purpose. Users are advised to back up their data to their own computers/external hard drives ASAP.
Here is a list of the file formats for images acquired on different BIRC microscopes and the relevant data handling procedures:
| Microscope name | Manufacturer | BIRC nickname | File format | Data handling | |
| 1 | Wide-field fluorescence/brightfield/DIC microscope | Zeiss | Edwina | .tif | MetaVue acquisition software (Molecular Devices) |
| 2 | Widefield fluorescence and phase contrast microscope for live time-lapse imaging | Olympus | Wendolene | .tif | MetaMorph acquisition software (includes MDA) |
| 3 | DeltaVision Image Restoration Microscope | Applied Precision/ GE/Leica | Wallace | .dv | SoftWoRx acquisition software |
| 4 | DeltaVision Image Restoration Microscope with FRAP/photoactivation module and environmental chamber | Applied Precision/ GE/ Leica | Totty | .dv | SoftWoRx acquisition software |
| 5 | CellDiscoverer7 (CD7) automated widefield high-throughput system | Zeiss | Admiral Collingwood | .czi | Zeiss ZEN Blue acquisition software |
| 6 | LSM 980 with Airyscan 2 – Confocal Microscope | ZEISS | Molly | .czi | Zeiss ZEN Blue acquisition software |
| 7 | Inverted LSM 780 laser scanning confocal microscope | Zeiss | Technotrousers | .czi | Zeiss ZEN Black acquisition software |
| 8 | Inverted LSM 880 Airyscan NLO laser scanning confocal and multiphoton microscope | Zeiss | Rocky II | .czi | Zeiss ZEN Black acquisition software |
| 9 | RS-G4 resonant scanning confocal system | Caliber ID | Cutlass Liz | .tif
.ims |
RS-G4 acquisition software |
| 10 | Facility Line STED/confocal system | Abberior | Pirate King | .obf
.msr |
Acquisition software 1: Imspector (Lightbox), ver 16.3.14287-w2129
– generates images in the .obf format Acquisition software 2: Imspector (BASE), ver 16.3.14287-w2129 – generates images in the .msr format
.obf and .msr files can be opened in either of the above acquisition software or Fiji |
| 11 | InstantSIM (iSIM) super-resolution system with Mizar TILT light-sheet | VisiTech/ BioVision/ Leica/ Mizar | Scopey McScopeface | .nd
.stk .tif |
VisiView acquisition software |
| 12 | OMX Blaze 3D-SIM super-resolution microscope | Applied Precision/ GE/ Leica | Reverend Hedges | .dv | SoftWoRx acquisition software |
| 13 | FV1000MPE upright multiphoton system | Olympus | Philip | .oif | Fluoview acquisition software |
| 14 | Spinning disk confocal microscope | Zeiss/ Yokagawa/ Spectral Applied | Bunty | .nd
.tif |
MetaMorph acquisition software |
| 15 | CellVoyager spinning disk confocal | Yokagawa/ Olympus | HMSBeagle | .tif | Acquisition software: CV1000
Single TIF files stitched with custom Fiji macros provided by the BIRC. |
| 16 | Widefield/TIRF system | Nikon | Piella | .nd2 | Elements acquisition software |
| 17 | Ultramicroscope II Light sheet | LaVision/ Miltenyi BioTec | Polly | OME-TIFF | Acquisition software: ImspectorPro
Imaris for assembling the images |