imaris exercises
TRANSCRIPT
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 1Volume rendering and visualization
Dataset: Nicklaus.MLE8
Reproduce the following representation:
Tips:Adjust contrast in MIP mode then take snapshot in shadow projection.
Play with frame settings
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 2Image Segmentation
Dataset: Shibutani_AttCor
Reproduce the following representation:
Tips:Adjust channel intensities to adjust optimal contrastPlay with the different rendering modesCreate Surfaces and SpotsUse the clippling plane
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 2 cont.Calculate the number of spots in the field of view.
Colour code blue surfaces accordingly with its sphericity.
Add a filter that selects only those surfaces over 226 µm3. What is the total number of blue surfaces?, how many has a volume larger than 226 µm3?
Explore using different filters in order to classify your surfaces or spots.
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 3Manual surface creation
Dataset: visu2crop
Reconstruct some structures of interest manually
Try our different drawing modes
Use Ortho Slicers to visualize the reconstructed structures
Tips: remember the short cut ctrl+space for drawing modeIsoline and Autofit might be good option in some cases
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 4Stablishing cell relationships
Dataset: kg01_STE.May05.ims
Only analyze the cells that aren’t touching the edges of the dataset.
Tips
Use Crop 3D under Edit menu
Use the nuclei to split the cells
Adjust the transparency of the Cells & Nuclei to show the Vesicles more clearly
Color-code the vesicles for whether they are located in the Nucleus or the Cytoplasm
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 4 cont
Statistics:
What is the cell with more vesicles?
Are the vesicles mainly located in the nucleus or cytoplasm?
How many vesicles are per nucleous?
Play with different statistical colour coded for nucleus and cells
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 5
TrackingDataset: movie3c-resamXY.ims
Detect multiple Spots Sizes
Find the best parameters for the tracking
Colour code spots depending on their diameter over time
Colour code tracks depending on their mean spead
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 5 contTrackingDataset: movie3c-resamXY.ims
Play with the display modes: Dragon tail, track style, and track discplacement
Do a classification of cells in order to visualise:
1- the ones with longer tracks
2- fastest cells
3- cells with straightest tracks
What is the average spot diameter?
What is the average speed?
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 6
Single object Tracking
Dataset: SwimingAlgae
Try using single spot tracking to create a small number of tracks
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Filament TracerDataset: PiramidalCell
Use Fully Automatic Autopath generation to trace an ROI of PyramidalCell.ims near the soma without detect spines checked. Use the default paramters. Then, use additional regions to add more to the existing filament, now with detect spines enabled... Experiment with using different settings in different regionsDon‘t forget you can shift-click to add/remove seed points for both dendrites and spints
Exercise 7
Play with different visualization modes, and colour coded statistics
Copyright © 1992-2010 Bitplane
IMARIS – Explore The Third Dimension!
Exercise 8Semi-manual Filament TracingDataset: SR-BRC-nosoma.ims• Skip Automatic Creation• Use the AutoPath drawing mode to draw
the dendrites• Use Rebuild Dendrite Diameter to detect
the dendrite diameter (but not spines)• Go back to Draw tab, set dendrite you
have drawn to the AutoPath starting point• Use Rebuild Spine Diameter to detect the
diameter of the spines you have drawn• Color-code the Spines according to some
statistic (e.g. Spine Volume)