non-destructive marking with objectj: practical examples
DESCRIPTION
Non-destructive Marking with ObjectJ: Practical Examples. Norbert O.E. Vischer Stelian Nastase. University of Amsterdam. History. W. Rasband. NIH Image. ImageJ. 1990. 1995. 2000. 2005. 2008. Non-destructive marking:. Object-Image. ObjectJ. N. Vischer. + S.Nastase. Project #1 - PowerPoint PPT PresentationTRANSCRIPT
Non-destructive Marking with ObjectJ:
Practical Examples
Norbert O.E. VischerStelian Nastase
University of Amsterdam
History
Object-Image ObjectJ
+ S.NastaseN. Vischer
Non-destructive marking:
1995
W. Rasband
2000 2005 20081990
NIH Image ImageJ
Project #1
Multi-parameter measurementsof bacterial cells
shown in hyperstacks
Phase contrast
1 µm
Escherichia coli
DNA
terminusoriginFluor. YFP
Fluor. CFP
Desired output:
axis length
mean diameter
constriction
relative spot positions
Composite object keeps
cell parameters together
13
Object Visibility in Hyperstacks
Link
… for setting up a project
ObjectJ provides 3 more windows:
Project Window
ObjectJ Tools
ObjectJ Results
Project Window: Defining Objects
SelectMoveConvert to ROI
KillCreate
User-definedpalette of
item types
Project Window: Linking Images
Drag
Discrete pixels
Discrete pixels
Continuous vector layer
File operations
Housekeeping
Special ObjectJ Windows
Project Macros
Demo
Analysis of fish eggs using ObjectJAnne-Christine Knag and Anders Thorsen, Norway
Atlantic cod, Gadus Morhua
1 mmEggs of Atlantic Cod
diameter = ?centre = ?
d = 148
• clean desktop• easy to detect bugs and artifacts• slide show• discussing results with others
• what you see is saved in two different files• understanding composite objects• macro programming
• stability• efficiency (large number of objects)• documentation and website
what we found useful:
what people find difficult:
what to improve
Conclusions:
bug
artifact
ObjectJ
Developed with NetBeansOpen SourceStill Betahttp://simon.bio.uva.nl/objectj
Credits:
Amsterdam:Stelian NastaseConrad WoldringhTanneke den BlaauwenDorus Gadella
Bergen:Anders ThorsenAnne-Christine Knag
Elsewhere:Wayne RasbandTudor organizers ImageJ community