Imaris Exercises

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



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



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.



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



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



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



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



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?



Exercise 6

Single object Tracking

Dataset: SwimingAlgae

Try using single spot tracking to create a small number of tracks



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



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)

Imaris Exercises

Documents

Transcript of Imaris Exercises