Histology images analysis


Hi guys!

I was actually wonder whether it is possible to create a Fiji plugin for the following situation:

I have to analyse several brightfield images of patients tissue samples obtained with a slidescanner Axio and saved as .czi

It would be really useful for the patient sample analysis to:

  1. load the full batch
  2. open the .czi files
  3. take a picture (.tiff/.jpeg) of the full overview with scale bar (e.g. 1mm)
  4. zoom-in to one ROI and take a picture with the new scale bar (e.g. 100 um)
  5. zoom-in this picture to a second ROI and take another picture with a new scale bar (e.g. 10 um)

would you guys be able to help me?

Thank you in advance


Hi Fabio,

a plugin would be overkill here.
A simple imageJ macro would be sufficient.
Problem is rather to specify the ROIs which I guess you would need to supply anyways manually. So a fully automated script does not make much sense.

In principle this is doable. But can be achieved just as well manually.
For a small number of images this might be fast enough.
Maybe look into actionbars to improve the efficiency of your manual processing: http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start



Thank you so much for the info!
I’m gonna try this macro, and I’ll come back to you!

Thanks a lot for the suggestion!