The Main menu commands are shown below.
The File menu is used to open images and to open the Resolve3D module that is used to acquire images.
Use |
To... |
Open |
Open an existing image file in an Image window. |
Connect to DMS Database |
Establishes a connection with a Data Management System database. Changes to "Disconnect from DMS Database" when already connected. |
Acquire (Resolve3D)
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Open Resolve3D (the softWoRx image acquisition module).
Note If you are using a stand-alone workstation version of softWoRx instead of a DeltaVision microscope system, Resolve3D opens in an emulation mode. |
Exit |
Exit softWoRx. |
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The Edit menu is used to open modules for editing image headers, combining images, and performing polygon mask image data extraction.
Use |
To... |
Header |
Open the Edit Image Header dialog box for viewing or editing. |
Copy Region |
Copy image data from an input source to an output destination. |
Image Fusion
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Combine two images of equal XY dimensions. Time points and wavelengths can be selected for the two input images that are combined into the output image. |
Cut Mask |
Cut the data contained within a polygon list (created with Edit Polygon or 2-D Object Finder) from the rest of the data. This data can then be written to a new data file or processed with other softWoRx functions. |
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The View menu is used to open modules that provide various views of image data.
Use |
To... |
Blend Colors |
Assign a color to each wavelength in the final image. |
Movie |
View data in a window as a sequence of movie frames. |
Slider |
Scroll through sections of all open windows simultaneously.
Note Only the windows that are being displayed at the time that you activate the Movie or the Section Slider will be affected. |
Scale All Windows |
Change the intensity scale of all open windows simultaneously. |
Quick Projection |
Quickly combine information from multiple Z sections. |
Trails Movie |
Track particle movement. |
Volume Viewer |
View all or part of your data in 3-D. |
Rotate3D |
Reorient input images arbitrarily in 3-D. |
Resample2D |
Reorient or resize image files section by section. |
Flip and Rotate |
Reorient images by flipping the image around the X or Y axis, or by rotating the image 90 degrees around the Z axis. |
Stitch |
Superimpose images that are organized as either a series of time points or Z sections. (Each time point or Z section is treated as a panel of the stitched image.) |
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The Process menu provides access to the quantitative processing modules.
Use |
To... |
Correct |
Correct systematic errors that occur during data collection. |
Calibrate |
Calibrate images acquired with Resolve3D to simultaneously compensate for a non-uniform field of illumination and a non-uniform CCD detector response. |
Deconvolve |
Use a Constrained Iterative Deconvolution algorithm to remove out-of-focus blur in fluorescence optical sections. |
Nearest Neighbor |
Use an approximate deconvolution approach for removing blur from optical sections. |
Equalize Time Points |
Allow the intensities of all other time points to be equalized in reference to a selected time point. |
Align Image |
Adjust images to one another, both in X and Y and rotationally. |
Task Builder |
Set up process chains in the Task Builder dialog box. |
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The Filter menu provides access to various 2D and 3D filtering modules.
Use |
To... |
Convolution |
Perform basic digital filtering, such as high-pass and low-pass filtering. |
Edge Enhance |
Use the image intensity gradient to enhance object boundaries. |
Filter2D |
Select from a suite of 2-D filters for image processing. |
Image Arithmetic |
Calculate an output image from one or two input images using one of several available operations. |
Enhance Contrast |
Scale the intensity of each pixel in the image based on the local mean and local contrast values calculated from the pixel elements that form a box around the pixel of interest. |
Threshold |
Remove all data in an image that is below a certain intensity cutoff value. |
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The Model menu provides access to tools that are used to create and display 3D models of features in the image data.
Use |
To... |
Edit Polygon |
Create 2-D polygons in an Image window for use in either defining a 3-D structure in another program or for cutting out a section of an image defined by polygons. |
2D Polygon Finder |
Create polygons around features in 2-D sections. |
3D Object Builder |
Create 3-D objects by associating 2-D polygons together, based on their overlap from section to section. |
3D Model (Optional) |
Create models of the structures in your image data. |
Straight (Optional) |
Cut tubular structures from a data set and display them as new data sets. |
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The Measure menu provides access to interactive measuring tools.
Use |
To... |
Distance |
Measure 3-D distances in real space or in pixel coordinates. |
Point Values |
Display information on the data in a window as you move the mouse over the area of interest. |
Line Profile |
Profile intensities along a horizontal or vertical line. |
Pick Points |
Create lists of points for each wavelength and/or time point. |
Chromatic Correction |
Correct for shifts in color that result from oil matching and other environmental conditions. |
Colocalization |
Create a scatter plot of results and measure the Pearson Coefficient of Correlation. |
Colocalization (ROI) |
Create ROI polygons from which a scatter plot and Pearson Coefficient of Correlation are derived. |
FRET Analysis |
Calculate Fluorescence Resonance Energy Transfer (FRET) and Net FRET. |
PK Analysis |
Display the recovery (or dispersion) of fluorescence in a photokinetic experiment (e.g., a Fluorescence Recovery After Photo Bleaching (FRAP) experiment). |
| Localization Image Analysis | Display the Localization Image Analysis window. Use this set of tabs to analyze, correct, and reconstruct images from acquired localization data. |
| Localization Results Viewer | Display the Localization Results Viewer window. Use this window to evaluate the results of the selected parameters, after running the localization analysis tool, by comparing the detected fluorophore positions to the original acquired image. |
| Localization Image Reconstruction | Display the Localization Image Reconstruction tool. Use this window to closely examine regions of interest within a localization image. |
| PSF Width | Display the PSF Width tool. Use this window to measure the PSF Width (sometimes called the "PSF size factor") value used as the input parameter for the Localization Analysis algorithm. |
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The Conversions menu is used to open modules for importing and exporting image data.
Use |
To... |
Import from TIFF |
Convert a TIFF image file or series of files to the DeltaVision format. |
Import from ISee |
Convert Inovision Isee" image files to the DeltaVision format. |
Import from PIC |
Convert BioRad MRC-600 Pic" image files to the DeltaVision format. |
Import from MetaMorph STK |
Convert MetaMorph STK image files to the DeltaVision format. |
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The Conversions menu is also used to open tools for managing OTF files.
Use |
To... |
Calculate OTF |
Calculate an optical transfer function (OTF) when a measured OTF is unavailable. |
Convert PSF to OTF |
Convert a measured point spread (PSF) to an OTF. |
Export to Text |
Convert softWoRx image data to a text (ASCII) format. |
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The Utilities menu is used to open miscellaneous tools for managing system configuration and monitoring system resources.
Use |
To... |
User Parameters |
Customize several variables that affect how softWoRx functions (applies to the account currently being used to run softWoRx). |
System Parameters |
Customize several variables that affect how softWoRx functions (applies to the system default settings used by all users). This function is password-protected.
Note User parameters take preference over system parameters. |
Archive Data to CD |
Archive image data to CD. |
softWoRx Queue Manager |
Manage deconvolution jobs. |
View Top CPU Users |
Display the processes using CPU time. |
Image Snapshot |
Start an image capture program to save all or portions of the screen. |
Revise Microscope Configuration |
View or revise the microscope configuration. (The revision function only applies to users of a DeltaVision system and is password-protected.) |
Lens Information |
Provide information about the lenses listed in the softWoRx lens database. This helps you to optimize microscope resolution and provides image resolution and measurement information. |
Revise Lens Database |
View or revise the lens configuration. |
Revise Convolution Kernels |
View or revise the convolution kernels. |
Review Plate Scan |
View the Plate Scan Reviewer window. |
Get System Logs |
Display the Get DV Logs window to view existing DV log files. |
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