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Transcript of Non-destructive Marking with ObjectJ: Practical Examples Norbert O.E. Vischer Stelian Nastase...
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Non-destructive Marking with ObjectJ:
Practical Examples
Norbert O.E. VischerStelian Nastase
University of Amsterdam
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History
Object-Image ObjectJ
+ S.NastaseN. Vischer
Non-destructive marking:
1995
W. Rasband
2000 2005 20081990
NIH Image ImageJ
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Project #1
Multi-parameter measurementsof bacterial cells
shown in hyperstacks
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Phase contrast
1 µm
Escherichia coli
DNA
terminusoriginFluor. YFP
Fluor. CFP
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Desired output:
axis length
mean diameter
constriction
relative spot positions
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Composite object keeps
cell parameters together
13
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Object Visibility in Hyperstacks
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Link
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… for setting up a project
ObjectJ provides 3 more windows:
Project Window
ObjectJ Tools
ObjectJ Results
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Project Window: Defining Objects
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SelectMoveConvert to ROI
KillCreate
User-definedpalette of
item types
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Project Window: Linking Images
Drag
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Discrete pixels
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Discrete pixels
Continuous vector layer
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File operations
Housekeeping
Special ObjectJ Windows
Project Macros
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Demo
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Analysis of fish eggs using ObjectJAnne-Christine Knag and Anders Thorsen, Norway
Atlantic cod, Gadus Morhua
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1 mmEggs of Atlantic Cod
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diameter = ?centre = ?
d = 148
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• 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
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ObjectJ
Developed with NetBeansOpen SourceStill Betahttp://simon.bio.uva.nl/objectj
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Credits:
Amsterdam:Stelian NastaseConrad WoldringhTanneke den BlaauwenDorus Gadella
Bergen:Anders ThorsenAnne-Christine Knag
Elsewhere:Wayne RasbandTudor organizers ImageJ community
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