Advanced Image Processing using Imaris ( ) Zentrum für Mikroskopie und Bildanalyse

Transcription

1 Advanced Image Processing using Imaris ( ) Urs Ziegler Zentrum für Mikroskopie und Bildanalyse

2 Imaris integrated modules Todays seminar Open and Save data Isosurface Contrast and Brightness Display Adjustments Navigation through data Slice Section Easy 3D Snapshots Spot detection Filament tracing Contour Statistics and Measurements Animations Surpass

3 Surface rendering: Isosurface Identification of voxels belonging to an object. The criteria for the identification is the grey value of the voxel: threshold value. grey level < threshold value = background grey level > threshold value = object surface voxel = voxel belonging to an object while some of its neighbors do not.

4 Isosurface Data displayed as a volume (MIP or Blend) with intensities adjusted that only structures of interest are visible Threshold in isosurface rendering

5 Isosurface Select a new isosurface Select channel Select if smoothing and / or background subtraction should be performed

6 Isosurface Select threshold (optional: split touching objects)

7 Spot detection Data displayed as a volume (MIP or Blend) with intensities adjusted that only structures of interest are visible Measure diameter of structures in slice mode

8 Spot detection Filter detected spots according to selected criteria (Quality ~ intensity at center)

9 Tracking spots 1. Select Track Spots over time 2. Select which type of motion model should be applied

10 Spot tracking Motion models Brownian Motion This algorithm models the motion of each Spot as a Brownian motion. This model is appropriate, if your Spots actually perform a Brownian motion. Autoregressive Motion This algorithm models the motion of each Spot as an autoregressive process. This model is appropriate if your Spots perform any kind of continuous motion. Filter detected tracks according to selected criteria

11 Filtering, statistics and counting Example: Chlamydia infected cells 1. Detect nuclei via spot function Counting cells based on DNA stained nuclei Evaluation of infection based on the size of inclusion (fluorescently labeled Chlamydia) Attention: DNA found in nuclei and Chlamydia Spots are only detected in the nuclei because of filtering for low intensity in channel 2 (green labeled Chlamydia)

12 Filtering, statistics and counting Example: Chlamydia infected cells 2. Detect inclusions via isosurface Counting cells based on DNA stained nuclei Evaluation of infection based on the size of inclusion (fluorescently labeled Chlamydia) Attention: DNA found in nuclei and Chlamydia Isosurfaces are filtered for size (>100um, green labeled).

13 Filtering, statistics and counting Example: Chlamydia infected cells View or export values / statistic Counting cells based on DNA stained nuclei Evaluation of infection based on the size of inclusion (fluorescently labeled Chlamydia) Attention: DNA found in nuclei and Chlamydia Individual objects can be selected

14 Animation Animation can be designed using keyframes which store scenes shown in the display. Frames between keyframes are interpolated. Add a keyframe Number of frames Keyframes (blue, white if selected) Save animation (format: uncompressed avi for ease of use)

15 Questions and Outlook Next lunch seminar: Tuesday, 20th of January 2009 Advanced Image Processing: Spot Detection Animation Generation If time: starting Deconvolution Questions and input: or

16 Imaris 7 floating licenses bought by several research groups (2005) License server maintained by the computing center: 2701@idlicense1.uzh.ch Maintenance of Imaris paid by the Center for Microsocpy and Image Analysis Download of Imaris and coordination for acquisiton of new modules and licenses at the University via the Center for Microsocpy and Image Analysis: :