Correlative image rendering
Prerequisites
Before starting this lesson, you should be familiar with:
Learning Objectives
After completing this lesson, learners should be able to:
Understand how heterogeneous image data can be mapped from voxel space into a global coordinate system.
Understand how an image viewer can render a plane from a global coordinate system.
Motivation
“In correlative microscopy the same specimen is imaged with multiple modalities. While this provides great opportunities for scientific discovery it poses some visualisation challenges. The various images may have different voxel sizes and different dimensionality and may be translated and rotated with respect to another. To tackle this challenge appropriate image viewer software and image data file formats must be chosen. To make those hoices it is important to understand the basic concepts of correlative image rendering, as well as know some concrete implementations.”
Concept map
Figure
Activities
- Explore the composite planar rendering of two (or more) (heterodimensional) images.
- Change the angle and extent (zoom) of the rendered plane.
- If the data contains both 2-D and 3-D images, observe and discuss how the 2-D image is rendered when “looking from the side”.
- For one (or more) of the images change the mapping from voxel space into the global space.
Show activity for:
MoBIE
Requirements: Fiji with MoBIE update site
- Open a MoBIE project containing correlative data
[ Plugins › MoBIE › Open › Open MoBIE Project... ]
Project Location
https://github.com/mobie/clem-example-project/
- Explore the transformation from viewer to global space:
- Log the current
dgT
andgvT
- BDV context menu:
Log Source Transforms
&Log Current Location
- Zoom in
- BDV:
arrow up
- Log
dgT
andgvT
again and appreciate that only thegvT
has changed.
- Appreciate that the first component of the
gvT
is bigger, corresponding to the higher zoom level.- Add another image:
- MoBIE UI: From the
tomogram
drop-down choosetomo_37_hm
and click[ view ]
- Appreciate that navigation (i.e. finding the
tomo_37_hm
image) in large correlative data sets is challenging.- Focus on the
tomo_37_hm
image:
- MoBIE UI:
tomo_37_hm
click[ F ]
- Explore heterogeneous voxel sizes
- Toggle off interpolation
- BDV:
i
(it should say “nearest neighbor interpolation”)- Zoom in a bit more
- BDV:
arrow up
- Move to the edge of the
tomo_37_hm
- BDV: Mouse
right button drag
- Alternatively copy below
gvT
transform into thelocation
field and click[ move ]
{"normalizedAffine":[0.4963397000728218,0.0,0.0,-108.59369157880992,0.0,0.4963397000728218,0.0,-152.83843100300004,0.0,0.0,0.4963397000728218,3.865989923867204E-4],"timepoint":0}
- Appreciate that the voxels of the
em-overview
are visible (and are larger than the voxels oftomo_37_hm
)- This information is encoded in the transformations from data space to global space (dgT):
- Explore heterodimensional (2D & 3D) rendering
- Look at the data from the side
- BDV:
shift y
- Zoom out until you see the edges of
em-overview
along the z-axis
- BDV:
arrow down
- Alternatively copy below
gvT
transform into thelocation
field and click[ move ]
{"normalizedAffine":[-0.0020015317086036193,-0.01932460609735281,-5.114194702548178E-19,6.3944917447396445,-5.114194702548184E-19,-7.789826789933008E-19,0.019427983168573904,-0.0015838942648179167,-0.01932460609735281,0.0020015317086036193,-7.789826789933008E-19,3.638083567375694],"timepoint":0}
- Appreciate that the voxels of
em-overview
are rendered 300 nm along the z-axis.- This is specified here
- Change the
dgT
(“registration”) of one image:
- Focus on
tomo_37_hm
- MoBIE UI:
tomo_37_hm
click[ F ]
- Log the
dgT
- BDV context menu:
Log Source Transformations
- Change the
dgT
oftomo_37_hm
:
- BDV context menu:
Registration - Manual Transform
- Follow the instructions to change the location of
tomo_37_hm
- Log the
dgT
again (s.a.) and appreciate that it has changed.
Assessment
Fill in the blanks
- TODO ___ .
- TODO ___ .
Solution
- TODO
- TODO
Explanations
Follow-up material
Recommended follow-up modules:
Learn more: