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Using Softworx Explorer Suite

SWESOpen SoftWorx Explorer Suite (SWES)

 

The browser window will open. This window will allow you to browse through your files, view them and perform basic functions such as deconvolution and saving as tiffs.

SWESIn the upper left of the browser there is a directory tree that you can use to find your files. The Z:\ drive is your folder on the Keck Facility server. You can work with those files just fine, but operations such as scrolling up and down through the stack will go more smoothly if you move the files to the Analysis-Multidimensional computer.

 

If you want to move your files to the Analysis-Multidimensional computer put them in a folder in C:\Users. Remember that any files over 3 months old can be deleted from the analysis computers at anytime!

 

SWES

When you select a folder in the directory tree, the Deltavision files in that folder will be shown in the right half of the browser window. When you select one of those files, the image will be shown in the preview window. You can scroll through the stack in Z using the scroll wheel on the mouse or by clicking on the image and moving the mouse up and down while holding down the mouse button.

The window in the lower left-hand corner of the browser lists the image properties.

You can open the image file in the viewer function of SWES by double-clicking on either the preview image or the file name.

Right-clicking on the preview image will give you several options, including turning channels on and off.

 

 

 

 

 

 

 

 

 

 

Deconvolving from the SWES Browser Window

Deconvolution will proceed just as rapidly whether the files are residing on the server or on the Analysis-Multidimensional computer.

SWESTo deconvolve a single file, right-click on either the preview image or the name of the file in the list. Select tasks --> Deconvolve.

In the next window, titled "Job List Review", you will see the file as being selected for deconvolution. Click "Start Jobs".

The lower left window will change to the Batch Jobs tab and list the file being deconvolved. Progress on the deconvolution is shown in the extreme lower right-hand corner of the SWES window.

The deconvolved (D3D) image will be placed in the same directory as the original file.

You can also select multiple images in a folder (hold down the Control key while selecting them) to be deconvolved. After selecting, right click and select tasks --> Deconvolve.

You can automatically deconvolve all the image sets in a folder by right-clicking on the folder in the directory tree and selecting tasks --> deconvolve. In the "Job List Review" window, you will see the files as being selected for deconvolution. Click "Start Jobs".

If you want to view or change the default deconvolution settings, double-click the "Deconvolution" setting in the "Job List Review" windowSWES That will bring up a window with lots of tabs to examine and/or change the deconvolution settings. If you make changes, click on "Save Settings" and those will be the settings used to deconvolve that particular file.

Saving Images in TIFF Format from the SWES Browser Window

Saving as TIFF will proceed just as rapidly whether the files are residing on the server or on the Analysis-Multidimensional computer.

To convert all the image planes of a single file, right-click on either the preview image or the name of the file in the list. Select tasks --> Save As TIFF.

In the next window, titled "Job List Review", you will see the file as being selected for Save as Tiff. Click "Start Jobs".

The lower left window will change to the Batch Jobs tab and list the file being converted. Progress is shown in the extreme lower right-hand corner of the SWES window.

The TIFF images will be placed in a new folder with the same name as the original file. That folder will be in the same directory as the original file. The TIFF images will have the same name as the original file, appended with the Z-plane or Time-point (FileName_Z000, FileName_Z001, etc.)

You can also select multiple images in a folder (hold down the Control key while selecting them) to be deconvolved. After selecting, right click and select tasks --> Save As TIFF.

You can save TIFFs of all the image sets in a folder by right-clicking on the folder in the directory tree and selecting tasks --> Save As TIFF. In the "Job List Review" window, you will see the files as being selected for Save As TIFF. Click "Start Jobs".

The "Save As TIFF" Task is set up to save all of the image planes and/or time-points as RGB (color) TIFFs. See below to change to saving as grayscale TIFF images.

If you want to view or change the default Save As TIFF settings, double-click the "Save As TIFF " setting in the "Job List Review" windowSWES That will bring up a window with lots of options to examine and/or change the Save As TIFF settings. If you make changes, click on "Save Settings" and those will be the settings used to deconvolve that particular file.

You can also use the Tasks function to make a quick projection of an image stack.

 

Contact Greg Martin at gvm@u.washington.edu for additional information. Suggestions and comments are always welcome!

© 2007 Keck Microscopy Facility, University of Washington