Server Access
WindowsXP
instructions as .pdf
Mac
OS
instructions as .pdf
|
Image Analysis Software
Download-able
Software We Recommend
LOCI
Bio-Formats downloadable plugin for ImageJ. See our helpful tutorial
on this topic.
Available
from or in the Facility
Huygens Pro from SVI (64-bit
Linux, available by remote desktop) -- Our prefered deconvolution package.
Documentation to get you started with remote desktop here.
Huygens
Essential for Deconvolution from SVI (Windows XP, available in the KCBD
site only) -- A simplified version of the Huygens deconvolution
software.
Imaris
from Bitplane (64-bit Windows only, available in the KCBD site only) --
powerful multi-dimensional image processing software. Ideal for
multi-dimensional rendering, particle tracking in 4D (volume over
time), neurite tracing, spine counts, and multi-dimensional measuements
(volume, area, 3D counts, etc.).
MetaMorph
from Molecular Devices (Windows XP, offline version available in the
KCBD site) -- used for image collection and for limited data
processing. Particularly good at pixel intensity graphing,
limited particle tracking (2D over time, NOT 3D).
OpenLab from
Improvision (Windows XP and Mac OS X, available in the KCBD site) --
used for image collection and for limited data processing.
SlideBook from Intelligent Imaging Innovations, Inc.
(Windows XP and Mac offline versions available at KCBD site)
-- used for image collection on the vert100 and both spinning disk
confocals and for limited data processing. Particularly suited to
3D and 4D image rendering and quick montage making.
Other
Software Packages
BioImageXD -- free open source
software for anaylsis of multi-dimensional images
ImageSurfer
-- free 3D rendering software
Blender --
multi-dimensional animation software. Fun, but NOT for image
rendering!
Return to top of page
|
ImageJ Macros
ImageJ is scriptable software. Click here for links to macros developed in
the University of Chicago imaging facility.
|
Software Tutorials
ImageJ
ImageJ Basics
Tutorial (dowloadable .pdf) -- Just downloaded ImageJ and wondering
what to do next? This is the tutorial for you! It covers
basic topics including how to open an image or stack of images,
adjusting brightness and contrast, how to make color and multicolor
merge images, adding scale bars, and how to make 3D and timelapse
movies. .pdf version of a PowerPoint.
ImageJ
Basics Tutorial, the movie (requires Adobe Flash) -- A movie
version of our famous ImageJ Basics Tutorial. Winner of the
ImageJ User and Developer Conference 2008 Video Tutorial Competition.
Download-able tutorial .pdfs for more advanced ImageJ functions:
Opening
files with the LOCI Bio-Formats plugin
Merging
colors beyond RGB
Making
montages
Basic
cell counting
Counting
objects by template matching
For even more advanced ImageJ tutorials, check out Tony Collins's
excellent ImageJ
for Microscopy manual. Links to additional ImageJ tutorials
and documentation can be found on the ImageJ documentation page.
Huygens Pro
Deconvolution Software
Using
Huygens Pro by Remote Desktop (download-able .pdf) -- Covers basic
aspects of running the Huygens Pro deconvolution
software, available on the Linux machine in KCBD 1250 or by remote
desktop. The .pdf also includes instructions on how to access Huygens Pro by remote desktop from
any UChicago network computer.
Return to top of page
|
Learn
More About. . .
Fluorophores and Staining
Table of common fluorophores
and fluorescent
proteins with their color and excitation/emission maxima.
Invitrogen/Molecular Probes fluorescence
spectra viewer is a web-based, interactive wavelength viewer.
Very useful for determining degree of overlap between fluorophores.
Trouble with autofluorescence in your samples?Autofluorescence Causes
and Cures
Post-Image
Processing
Image
manipulation ethics
Colocalization
JACoP
for ImageJ, the original reference -- Everything you ever wanted to
know about colocalization, but were afraid to ask.
Return to top of page
|
Protocols
(help us fill out this section!)
Tips for
successful imaging -- Everybody wants beautiful, scientifically
valid images. Here is a little .pdf we put together to help you
get there. Read this BEFORE you start your experiment, it will
make a world of difference!
Return to top of page
|
Links
|
|
|
|
Contact Information
Vytas
Bindokas, PhD
Facility Director
Technical Director, AB-129
773.702.4875
vbindoka@bsd.uchicago.edu
Shirley Bond, MA
Technical Director, KCBD 1250
773.834.2639
sbond@bsd.uchicago.edu
Christine Labno,
PhDTechnical Director, KCBD 1250
773.834.9040
ccase@midway.uchicago.edu
Main Hospital Building
(Vytas)
Abbott Memorial Hall
Room AB-129
Knapp
Center
for Biomedical
Discovery
(Shirley & Christine)
First Floor, Room 1250
Core Support
Office of Shared
Research
Facilities (OSRF)
Cancer Research Center (UCCRC)
Intellectual and Developmental
Disabilities Research Center
(IDDRC)
Digestive Diseases Research
Core Center (DDRCC)
|
