Measure Intensity Without Spots

Measure the signal in a channel in areas defined by the stained nuclei in another channel. Remove the bright spots when measuring the signal.

The source code in git-hub can be found here.

Getting started

You must have MorphoLibJ and BaSiC installed.

To install the tool download the file measure_intensity_without_spots.ijm and put it into the folder macros/toolsets of your FIJI installation. In FIJI, select the measure_intensity_without_spots-toolset from the more tools button >>. On the toolset, click on the Install or Update Tool (the rightmost tool of the toolset).

Note: In case you do not have jython installed the first time you run the installation, only jython will be installed. You then have to retsart FIJI and click on the Install or Update Tool again.

After the installation finished, restart FIJI. Select the measure_intensity_without_spots-toolset from the >>-button of the ImageJ launcher.

• The first button (the one with the image) opens this help page
• The c-button exports the images from a .htd-file to a tif-series with each well as a stack
• The r-button runs the BaSiC-plugin on the tif-stacks, to correct the background
• The m-button measures the signal in the active image
• The j-button positions the image around the label whose line is selected in the results table.
• The br-button run the export and background correction on a batch of htd-images
• The b-button runs the processing and measuring for a batch of htd-images

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