Uploading Data into Amira

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Revision as of 18:39, 2 September 2011 by Brewski (Talk | contribs) (How to)

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Acceptable Data Formats

Amira will only accept specific file types including TIFF, JPEG, SGI-RGB, ACR-NEMA, and DICOM. If the data you want to upload into Amira is in any other format, it must be converted to one of the aforementioned file types. Do this using Photoshop.

All images imported into Amira must also be greyscale. Change colour images to greyscale using Photoshop as well.

How to

IMPORTANT: be sure that all data is in acceptable form and is stored sequentially in an easily accesible folder

1. Open Amira

2. Click the green Open Data... button in in the "Pool" section. This will open a load file menu in a new window.

3. In the Load File Window, find your folder of stored greyscale image data (converted from Photoshop -- see above). Make sure that all data is in the correct sequential order that you would like to interact with it in. Highlight all data to be included in this Amira file by clicking the first item, holding shift and then clicking the final item. Click LOAD. A new image read parameters window will then pop up.

4. Within the image read parameters window you will be able to define the size of each data point or Voxel (a 3D pixel). Use your image's pixel size and height to choose an appropriate pixel size (length X width X height)to maintain the anatomical integrity of your model under the resoultion heading. Under the import heading within this window change the channel conversion option from color field to channel 3. This is very IMPORTANT. Click OK

5. A new green bubble will appear below the open data button in the pool window titled after the data set you just entered. This is your data set now associated with this file.

6. Right click your green data set box and choose Labelling > LabelVoxel from the dropdown menu. This will open a red box called LabelVoxel attached to your green data set box.

7. Change from the pool view by selecting the segmentation button above the pool section. The segmentation button looks like 3 data slices stacked vertically upon eachother. It is fourth from the left.

8. You are now in segmentation view. In the section below the segmentation button, ensure that the Image Data is consistently named with your data set. Click the new button to the right of label data. This will generate 2 new materials in the white box below materials entitled exterior and inside.

9. You are now ready to begin manual or automatic Segmentation in Amira.

If this series of steps doesn't work and you are trying to import several files (Amira gives you a notice referencing LDA), you may need to make some adjustments within Amira to accomodate Large Data Sets

If you find that the images you've uploaded as slice data are not in a desired orientation visit Viewer Options in Amira for instructions on how to chage slice orientation.

NOTE: You are not able to add extra/additional data slices into your data file within amira after your initial upload. Make sure that you always upload more slices then you think you will need. If you attempt to add in new slices, they will appear as a second data set (green bubble) that can be interacted with separately within your Amira File.

Back to Using Amira