Grant Planning & Data Management

General Documentation for Grant Proposals

Summary of Data Types and Accessibility Options

Detailed information can be found in the Data Management & Share Plans reference document above.

Biomedical/Research Images Acquired on the Zeiss Imaging Platform
(710, 800, Elyra, Axioscan 7, Cell Discoverer 7)

*.czi image files contain the following Meta Data
  • Image settings: size, pixel type, scale (x,y,z), annotations
  • Microscope Settings: microscope, objective, reflector, contrast method, fluorescent dyes selected
  • Camera Settings: camera, binning, exposure time, bit depth
  • Document Info (optional, must be entered by researcher): title, subject, keywords, recording date, user information. ** these may facilitate file organization, sorting sharing.
*.czi files (Zeiss) may be read using open-source software. 
Individual repositories have specific requirements for acceptable file formats. If required by a repository, conversion of image files to opensource file formats such as OME tiffs (Open Microscopy Exchange) can be used to preserve meta data in a universal file format. This option is available in most programs readily interacting with *.czi files.
https://imagej.net/formats/bio-formats
https://imagej.net/software/fiji/downloads
https://www.zeiss.com/microscopy/en/products/software/zeiss-zen-lite.html
https://qupath.github.io/


Biomedical/Research Images Acquired on the UltraMicroscope II
(lightsheet microscope)

OME Tiff or *.IMS (IMARIS file) contain the following Meta Data
  • Light Sheet Microscope meta data is stored in the first image (only), do not delete this file.
  • Image settings (geometry): date, time, size, scale (x,y,z)
  • Parameters: channels, display settings, laser settings, filters, x,y,z acquisition settings.
  • The system currently registers the 515 nm laser as a 405 nm. This is incorrect and awaiting a software update from Miltenyi.
  • The acquisition software (Imspector) can only display one image tile. Complex images must be reconstructed in IMARIS or FIJI.
Mosaic images can be stitched together using ImageJ/FIJI BigStitcher (OME Tiff) or using the IMARIS stitch program (requires initial storage as, or conversion to *.ims file type). 
IMS files can be viewed using free viewer software.
https://imaris.oxinst.com/imaris-viewer
https://imagej.net/plugins/bigstitcher/advanced-stitching


Biomedical/Research Images Analyzed using Image Analysis Workstations

IMARIS Software (IMS)
Images are converted to *.IMS files for analyses. These new files contain the following meta data.
  • Dataset: Contains the actual image data (by channel and timepoint, from the original image meta data).
  • Dataset Info: Contains descriptive image parameters for IMARIS. A creation histogram reports display and analysis settings for IMARIS image file.
  • Thumbnail: 2D thumbnail of the image.
  • See detailed summary: Imaris File Format - Imaris - Oxford Instruments (oxinst.com)
HALO Software
Images are only read by HALO, there are no ‘HALO’ image files.
  • HALO databases containing display and analysis settings are generated for each analyzed image.
  • To access these settings, go to Studies tab, select images, advanced settings tab, select settings and analysis steps performed, export details (input and output info) as a *.csv file.


Transferring/Working with Large Image Data Files

Please ensure adequate storage space and upload times when transferring imaging data.  The AMCF has installed 10 Gb ethernet connections between the new instrumentation (Axioscan whole slide imager, Light Sheet Microscope) and the Data analysis room. Additional high-speed connections will be established as quickly as possible. Many locations on campus are 10 Gb 'ready,' not actively installed/configured. Researchers should verify individual transfer capabilities in their location/building and plan accordingly.

Table from UltraMicroscope II Users Guide:
ultramicroscopetable.png