Hi Ofra,
Here are some instructions with two different options that should both do what you want (text pasted in below). They were created by one of our users, but I have not had the need to use them in a few years, so all I remember is that importing takes some patience -- the Pannoramic viewer files can be quite large.
Best,
Christine
Created 020613
Pannoramic Viewer to ImageJ Instructions
Created by Diana Doeing, MD, from Steven White’s lab at the University of Chicago.
Open Pannoramic Viewer.
Open slide of interest (see “slide info” after opening slide file for label)
Outline “annotated” section of slide that you wish to export. Save as “(new title)“
Then go to (File -> Slide export (CTRL+E))
Select the annotated file (see new title that you saved it as)
Then Save as to PC/Mac or external HD (will be exported as a tiled TIF file)
Next open the newly exported file using PHOTOSHOP or Preview (for Mac) and resave or export as a .tif file again (new name) – this will “untile” the image so that it can be opened in ImageJ
Transfer file to external HD and back up on second drive (files will be large)
Next go to imageJ and select File-> open (go to last file that was saved from PHOTOSHOP or Preview or Windows Paint)
Or option 2:
Image I/O plugin bundle installation for ImageJ will work with Pannoramic export
tiled TIF files so that you may open them directly via ImageJ.
One of most relevant:
http://ij-plugins.sourceforge.net/plugins/imageio/index.htmlThe jimi plugins can also be found on the ImageJ website:
http://rsbweb.nih.gov/ij/plugins/jimi.htmlDownload the following plugins:
ij-ImageIO_.jar
Jimi_Reader.class
Jimi_Writer.class
jimi.jar
Then copy and paste them into the plugins folder for in the ImageJ program file
folder on your computer. Next re-open ImageJ. Go to Plugins. Choose compile
and run... and select “ij-ImageIO_.jar”
Then go back to plugins tab. You should now see Image IO in the drop down
menu. Select this, then Open. You can now open your tiled .TIF annotated file that
you exported from Pannoramic Viewer. This obviates the need for the additional
step of resaving the file in a program like Preview or Photoshop.
--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
(773) 834-9040 (phone)
________________________________________
From: ImageJ Interest Group [
[hidden email]] on behalf of Ofra Golani [
[hidden email]]
Sent: Sunday, July 19, 2015 7:33 AM
To:
[hidden email]
Subject: Reading 3D Histech digital slides (.mrxs format)
Hi,
Is there a way to open in ImageJ digital slides acquired using 3D Histech digital scanner.
The files are of .mrxs format which accompanies by a folder of many .dat files.
We now use Panoramic Viewer to export each slide independently into tiled tif file, because Panoramic Viewer export cannot be batched.
As we need to run image analysis on many slides the export step is very time-consuming and we want to avoid it.
Thanks,
Ofra Golani
BioImaging Analyst
Biological Services Department
Weizmann Institute of Science
Tel: +972-8-934-5177
[hidden email]
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