Combining the python 3D viewer with FIJI
10.07.2021
Montpellier Ressources Imagerie
Volker Bäcker
:) solves the problem :( can not be automatized
3D Maxima Finder
from the 3D Suite ImageJ
:) can be automatized :( hard to set a threshold with out seeing the consequences in 3D
data = getResulsTable()
display(data)
cal = IJ.getImage().getCalibration()
coords = np.delete(data.values,[3], axis=1)
icoords = [[z, y, x] for [x,y,z] in coords]
zFactor = cal.getZ(1) / cal.getX(1)
points_layer = viewer.add_points(icoords, size=1, scale=[zFactor, 1, 1])
from ijpb.fiji.IPythonProxy import IPythonProxy
p = IPythonProxy()
p.run("import napari")
p.run("from PyQt5 import QtCore")
p.run("viewer = napari.Viewer()")
p.disconnect()
jupter_connection_file
python_executable
in IJ