SmartCaptureLite is a free to use ImageJ plugin. Although written with existing SmartCapture users in mind, SmartCaptureLite may be of use to anyone working with multichannel fluorescence images.


Existing SmartCapture users should check the section on SmartCapture Reader for information on transferring images from SmartCapture 3 to SmartCaptureLite


Download SmartCaptureLite


Composite Adjuster


Use Composite Adjuster to interactively adjust the normalisation levels and colours in a composite image.


Features

  1. BulletInteractive adjustment of normalisation levels.

  2. BulletSet channel colours for the low and high level (a colour ramp lut is generated between the two colours, control click on the histogram sliders)

  3. BulletDisplay levels as absolute values or as population percentages

  4. BulletMacro scriptable and recordable

  5. BulletWorks with Byte, Short and Float CompositeImages

  6. BulletWorks with 4 and 5 dimensional stacks with live update of histograms and ability to change settings whilst animation is in progress.



 

Watch the Movies

Instructions

A min/max slider and histogram are displayed for each of the image channels. Control or right click on a histogram to access the context menu
to set the histogram low and high colours or swap the histogram colours.


Use the Copy button to copy the current settings then select a new image and apply those settings using the Paste button.


Create an ImageJ macro for current settings with the Record button.


Use the Make Composite button to convert a non Composite Image into a Composite Image.


At the bottom of of the Composite Adjuster window is a small area that displays a message of the day. This message comes direct from our website (if it can be reached) and we will use this to notify you when new versions are available.


You can try Composite_Adjuster with this 6 channel, 16bit Composite (supplied courtesy of Dr. Fengtang Yang, Sanger Centre, Cambridge, UK.) available on our downloads page.


Under the Preferences tab
you get the following options:


Always on top: Cause the Composite Adjuster window to float on top of all other windows. This can be useful when you have lots of images you wish to adjust and you want to avoid the Composite Adjuster becoming buried under the image windows.


Ignore animated windows: Check this to disable the Composite Adjuster during animation. This may be useful If you are using a slow machine where live display of histograms in Composite Adjuster may degrade performance during animation.


Stretch histograms: Check this option to stretch each histogram to the maximum available display width. Uncheck this option to display all the histograms with the same minimum and maximum values.


Use % values:  Display values as percentage of population rather than as absolute pixel values. Used with Record button, you can easily create a macro for making images of similar subject matter but differing exposure values conform to a similar appearance.


Scripting

Composite Adjuster can be scripted, this can be useful for applying a set of composite image settings to multiple images. here is an example script:


run("Composite Palette", "mode=composite");

run("Composite Palette", "channel=1 active=true low-colour=0x0 high-colour=0xff0000 low=88.52% high=100%");

run("Composite Palette", "channel=2 active=true low-colour=0x0 high-colour=0xffff00 low=86.74% high=100%");

run("Composite Palette", "channel=3 active=false low-colour=0x0 high-colour=0x999999 low=83.31% high=100%");

run("Composite Palette", "channel=4 active=true low-colour=0x0 high-colour=0xff00 low=88.7% high=100%");

run("Composite Palette", "channel=5 active=true low-colour=0x0 high-colour=0xff low=90.22% high=100%");

run("Composite Palette", "channel=6 active=true low-colour=0x0 high-colour=0xff00ff low=89.61% high=100%");


# use channel=all to apply a setting to all channels

run("Composite Palette", "channel=all active=true low=90% high=100%");


SmartCapture Reader


An ImageJ plugin to read multi page TIFF files as exported from SmartCapture 3. This is like the ImageJ facility for reading TIFF files but it also sets the name and colours for each channel and will open the images as a CompositeImage.


SmartCapture 3 users should use the ExportSmartCapture4 script to export images from SmartCapture 3 to SmartCapture 4


SmartType Reader


An ImageJ plugin to read SmartType karyotyper files. The ROI manager is populated with the boundaries of each of the chromosomes.

 

SmartType is an inexpensive yet full featured karyotyping system. The express version is available free of charge and allows for 30 minutes use at a time. Karyotype files may be saved and printed. see SmartType


Updater


Update SmartCaptureLite to the latest version (located on this web site). See Notes


Run Updater periodically to check you have the latest version.


Grid Overlay



A simple ImageJ plugin to draw a grid of user specified size and colour on the non destructive overlay of an image.



Barrel Shifter


An ImageJ Plugin filter implementing an image barrel shift operation. It presents a dialogue requesting numerical values for the x and y translation. If a ROI is defined, the dialogue defaults to values that will translate the top left of the ROI to the origin. If there is no ROI defined, the dialogue defaults to values that will translate the centre of the image to the origin.

Barrel_Shifter is macro recordable and can be applied to the currently selected slice or all slices of a stack.

   


Barrel shifting an image by [x,y] will translate the image by [x,y]. Pixels that fall off the left or right hand edge of the image are wrapped around to reappear the right or left of the image and pixels that fall of the top or bottom of the image are wrapped around to reappear on the bottom or top of the image.


Set Scale


The SmartCaptureLite Set Scale ImageJ plugin sets the pixel size of an image just as the built in ImageJ Set Scale command does. The difference being that the SmartCaptureLite version sets the pixel size based on the camera, binning and objective you used to capture the image.


To use SmartCaptureLite Set Scale


  1. BulletOpen the image that you wish to set the scale for

  2. BulletChoose Set Scale from the SmartCaptureLite plugin in the Plugins menu.



  1. BulletSelect the appropriate camera, binning and objective magnification from the dialog

  2. BulletClick OK

  3. BulletSelect Scale Bar... from the Tools submenu of the ImageJ Analyse menu


Leave Global unchecked to apply the scaling to current image only. Check Global to have the scaling applied globally to all images and applied to images that you subsequently open.


Export to SmartType


Use the Export to SmartType plugin to transfer images of metaphase from ImageJ to the SmartType karyotyper.


Any open images with duplicate names are renamed by appending a number to make the image names unique. A dialog is displayed allowing you to nominate up to 3 of the open images. The nominated images are converted to 8 bit and cropped according to any ROI defined on the image. The cropped converted images are then sent to SmartType. SmartType must be running and have a case SmartType open to receive the metaphase images. Select brightfield or fluorescence from Image sense menu as appropriate to your image type.




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Disclaimers and Notes
Although created for our existing customers we are pleased to offer these plugins free of charge to all. All these plugins are in an early stage of development and we are experimenting with various means of deployment. Presently SmartCaptureLite checks an online security database to establish what features are enabled. All features in SmartCaptureLite are enabled for all users!. 
Rest assured the Security System used by the DSUK ImageJ plugins logs no information about you or your system. Here’s how it all works:
The online security database is just a list of what features can run against what security keys. The plugin reads this database and then compares it against the security keys that you hold. Security keys are gathered from local information (e.g. the MAC address, the system properties for user.name etc).
This security information is not logged anywhere, either locally or on our website.
SmartCaptureLite Release Notes
http://www.dsuk.biz/Downloads/SCReleaseNotes.htmlshapeimage_2_link_0

  

Update: Tuesday, 29 November 2016