EMBL BioImage Data Analysis
EMBL BioImage Data Analysis
|RT @haesleinhuepf: Thanks @gomez_mariscal for contributing to our #NEUBIAS satellite meeting! Looking forward to seed #DeepImageJ in action… |
About 1 day, 21 hours ago by: Kota Miura (@cmci_)
|RT @EMBLEvents: #BioimageAnalysis is a keystone of biological research. Due to the complexity of data, it's likely that #ImageAnalysis algo… |
About 2 days, 1 hour ago by: Kota Miura (@cmci_)
|RT @gomez_mariscal: Excited about introducing #deepImageJ during the #NEUBIASSatelliteMeeting
@NEUBIAS_COST @COM… |
About 2 days, 12 hours ago by: Kota Miura (@cmci_)
|@fab_cordelieres @NEUBIAS_COST @BIC_Bordeaux :) |
About 2 days, 19 hours ago by: Kota Miura (@cmci_)
|@haesleinhuepf @TalleyJLambert @Ulrike_Boehm "The intensity of this image sequence..." |
About 2 days, 22 hours ago by: Kota Miura (@cmci_)
|RT @focalplane_jcs: Hi all, my name is Christos @KyprianouChr and I am the Community Manager of the FocalPlane site, launching this summer.… |
About 6 days, 19 hours ago by: Kota Miura (@cmci_)
3DViewer is a great plugin that enables interactive viewing of 3D structure. It has many useful functions including 3D time lapse visualization.
The plugin has one problem when used in some of Windows XPs (not in Vista, Win7, Mac OSX), and the symptom is like this:
On start up, the rendered volume is zoomed-up too much, so that one could not find where the object is. Zooming tool (magnification tool from the menu bar) also does not work, so one must adjust the zooming level from scripts.
Similar problem is reported here.
By the way, a test for the Java3D is OK (could be tested via some pages such as here).
importPackage(Packages.ij3d); importPackage(Packages.javax.media.j3d); importPackage(Packages.javax.vecmath); imp = IJ.getImage(); StackConverter(imp).convertToGray8(); univ = new Image3DUniverse(); univ.show(); c = univ.addVoltex(imp); t3d = new Transform3D(); t3d.setScale(0.002); c.applyTransform(t3d);
Alternatively, one could also change the zooming from the menu. Following is an example of doing so.
I made further tests of 3Dviewer with various windows machines and in most cases, it worked fine.
“flybrain” sample 3D stack, accessible via File > Open Sample > Flybrain, was used. THis 3-channel image was separated with channels and used the green channel stack for the test.
Comparison of Java3D properties in XP machines (3 to 5) is in a table (link).
I still cannot figure out why No.3 machine is not working. A hint could be that the GUI tool for zooming (magnifying glass tool) does not work at all in case of machine No.3, but in all other cases it worked fine.
Another case of problem with 3Dviewer I encountered was a bit more straight forward. When DirectX was uses as render, then the object does not appear in the canvas. For this, one could start-up fiji with some option as below to force use OpenGL. In my case, I wrote a single line batch file to start-up fiji.
c:\Fiji.app\fiji-win32 -Dj3d.rend=ogl --console --mem=500m --More details on options are available here.