How to automatically save output window from Identify Primary Objects function

Hi,
The output window from 'identify primary objects is such a good visual summary of the data, I would like to basically screenshot the whole window - export both the images and table into one png/pdf as part of the pipeline and save it. Is this possible as part of the pipeline, so then at the end of the analysis each original image has its own summary image?

Also in programs like FIJI you can increase the brightness/contrast of the images, is there a way to do that here as a prior step to make the identification of objects better- i have a dull fluorescent stain that is not being picked up.

Thanks!

1 Like

Hello there,

For saving the color segmentation output: you can use module SaveImages like this:

mages**

For increasing the brightness/contrast, you can use module ImageMath with multiplication or log transform the signal intensity.

Hope that helps

Hi Monica,
Unfortunately saving the whole window is technically difficult to do in an automated way, so we don’t allow that option. Sorry!

To address this part of your question:

increase the brightness/contrast of the images, is there a way to do that here as a prior step to make the identification of objects better- i have a dull fluorescent stain that is not being picked up.

Most likely you don’t want to use ImageMath or some other mechanism to change the brightness/contrast. Instead, focus on the settings in the IdentifyPrimaryObjects module - specifically, adjust the thresholding settings to be more lenient. Take a look at the help buttons near the thresholding options to learn more and post back if you have particular Qs!

Anne