[slicer-users] Loading Confocal Microscopy Images into Slicer 3D

Curtis Lisle curtislisle at knowledgevis.com
Fri Feb 5 19:37:50 EST 2010

Dear Stephen,
I have used Slicer3 in microscopy applications and am able to load a TIF stack into Slicer.  Slicer3 is smart enough to load all TIF files inside a single directory if they are named consistently, such as   myData_zXXX.tif, where XXX is replaced by a slice number (myData_z001.tif, myData_z002.tif, etc.).  I use the Volumes module, select the first file (slice 001) only, then click "Center Image" and "Apply" and Slicer is smart enough to load the whole stack.    This may be what you are doing already and it might be a strange filename that is confusion Slicer.  Please provide more information about how your files are organized and I might be able to suggest what is happening.  Good Luck!


Curtis Lisle
curtislisle at knowledgevis.com

On Feb 5, 2010, at 2:17 PM, Stephen McClendon wrote:

> I am having a problem with loading confocal microscopy tiff image slices into 3D slicer. I have tried to load data and volume into 3D slicer but it won't read my images. I have also created a Quick time slide show or .mov and also cannot import it into 3D slicer. I followed your confocal microscopy tutorial but it only shows how to load the .pic data from Cell Centered Database. Is there a way to create a file from my tiff slices so that I may manipulate it in Slicer 3D? Any help you can offer will be greatly appreciated.
> Stephen McClendon
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