30. Insight as Plugin ImageJ/Fiji

To test in: ImageJ, Fiji

Purpose of the test is to check that the OMERO insight works as plugin for ImageJ/Fiji and the bioformats_package.jar or loci_tools.jar missing is not causing a crash.

Test on Linux as well as Windows (XP and Win7 if possible)

Download the OMERO.insight-ij* build and unzip it [or copy it into] in ImageJ/plugins folder [InsightIJI001]

ImageJ and ImageJ2

Note: You can download ImageJ2 from https://imagej.net/Downloads.

Add neither bioformats_package.jar nor loci_tools.jar to the Plugins folder of ImageJ (or ImageJ2). If it is there, remove it.
Start ImageJ (or ImageJ2) and go Plugins > OMERO > Connect to OMERO
- Check that a popup appears indicating that bioformats_package.jar or loci_tools.jar is missing.[InsightIJI002]
(For the release-day testing only.) Click on the hyperlink in the popup and Check it brings you to the last release version of Bio-formats. Download bioformats_package.jar [InsightIJI005] from this Bio-formats release Download page which is being coupled with the OMERO for the release, e.g. https://downloads.openmicroscopy.org/bio-formats/<version> . Note that this does not have to be matching version with the OMERO version, as Bio-formats is decoupled from OMERO.
(For non-release-day testing only.) Download bioformats_package.jar from CI in case you are testing a Bio-formats PR.
Quit ImageJ. Copy bioformats_package.jar into Plugins folder of ImageJ [InsightIJI001].
Restart ImageJ (or ImageJ2), and go Plugins > OMERO > Connect to OMERO
- Check the bioformats_package.jar version. To check the bioformats_package.jar version, open ImageJ (or ImageJ2), go Help > About Plugins > Bio-Formats Plugins or Help > About Plugins > LOCI Plugins [InsightIJI004].
- Check that Insight splashscreen is displayed.
- Check that if you rename the bioformats_package.jar to bioformats_package<substitute-any-string>.jar and restart ImageJ, and Connnect to OMERO` again, the Insight plugin still starts and no warning is being displayed.
Log in.
Go to the left-hand pane and select an image or import one if no images available.
Double-click on the image and then click OK in the Bio-Formats Import Options window [InsightIJI006].
- Check that the image opens in ImageJ [InsightIJI007].
Replace the bioformats_package.jar with loci_tools.jar and repeat the steps 3 (on release day only) or 4 (non-release day only) and 5, 6, 7, 8 and 9 (on both release and non-release days).
Put both bioformats_package.jar and loci_tools.jar into Plugins folder and restart ImageJ (or ImageJ2).
- Check that a duplication warning appears [InsightIJI007b].
- Check that you can still connect to OMERO and open an image.
Go through all steps using ImageJ64 and the platform independent version of ImageJ (download from ImageJ homepage).

ImageJ - ROI and OMERO upload (This section is just pre-release testing scenario (unless stated otherwise), do not do on release day, on release day go to section Fiji)

Open an image in ImageJ, draw regions using IJ toolbar on a particular z, t and c plane and click Analyze > Tools > ROI Manager. Each time you draw a new region click Add in the ROI Manager (The key t can be used as keyboard shortcut).
- export the image using Plugins > Bio-formats > Bio-formats Exporter to the local drive on your machine
- make sure the Export ROIs tickbox in the second dialog (Bio-Formats Exporter Options) is ticked BY DEFAULT
- close the image
- close the ROI Manager
- reimport the saved image using Plugins > Bio-formats > Bio-formats Importer, selecting the checkboxes Display ROIs, Display OME-XML metadata and Display Metadata in the Bio-formats importer options)
- Check that the OME-XML has all the saved ROIs listed as shown in example below
- Check that also the Shape Properties are listed in the OME-XML, for example StrokeColor and StrokeWidth. (See example below. Note: Shape FillColor is not being saved.)
- Check that when you tick the Show all tickbox in ROI Manager you see the regions just as you saved them on the image

example of OME-XML with Shape Properties:

<ROI ID="ROI:0:0" xmlns="http://www.openmicroscopy.org/Schemas/ROI/2015-01">
<Union>
<Shape FillColor="-16776961" ID="Shape:0:0" StrokeColor="65535" StrokeWidth="13.0" StrokeWidthUnit="pixel" Text="0001-0052-0076" TheC="0" TheT="0" TheZ="0">
<Rectangle Height="49.0" Width="91.0" X="31.0" Y="28.0"/>

Import the image you created into OMERO (using OMERO.insight). - Check that the image has regions as you have drawn them in ImageJ and the regions are correctly displayed in Insight and Web.
Repeat steps 1., 2. this time draw regions using IJ toolbar and Image > Overlay > Add selection or use the shortcut cmd B. Note that any regions in ROI Manager will be ignored in case the image has an Overlay to it. Do this workflow also for a stack (not hyperstack) image, e.g. test_images_good/tiff/QA images/Artificial_xyt_8bit.tif and for a hyperstack image (e.g. a multi z, c, t dv).
Open an image in ImageJ, create a rectangular region, and make a crop (Image > Crop).
- create a region in the cropped image and go Plugins > OMERO > Save Image(s) to OMERO
- Check that the Data Manager of Insight opens followed immmediately by Importer [InsightIJI007c]
- Select in a row both the radio button options in the Importer Add image from current window and Add image from all image windows
- Check that when you click Add to Queue the image(s) gets added to the right-hand pane of importer according to the option of the radio button which you selected.
- Do not create a new project nor select an existing one, and Check that after you imported, you have the image in Orphaned folder.
- Now create a new Project or select an existing project and use the default New From Folder option for Dataset and
- Check that after import, a new Dataset has been created under the Project you selected/created with the name identical to the folder containing the image opened in ImageJ (e.g. if you opened the image in ImageJ from users/your_name/localimages/ on your machine, the name of the Dataset should be localimages)
Open 2 images in ImageJ from your local drive and combine the 2 images (Image > Stacks > Tools > Combine). - go Plugins > OMERO > Save Image(s) to OMERO - Check that the generated image can be added to the queue and imported.
Testing Save ROIs to OMERO feature
- open an image from OMERO in ImageJ and also
- open another image, this time from your local disk (not from OMERO)
- draw ROIs on both images, add them to Overlay and select Save ROIs to OMERO
- in the first dialog select Save image from all open windows option and click Save
- Check that another dialog pops up [InsightIJI007e] asking you whether you want to also upload images not yet stored in OMERO
- select Yes and Check that an Import Location... dialog [InsightIJI007f] pops up for selection of P/D to import the image to
- select an existing P/D or create a new P/D and click Add to the Queue
- Check that import immediately starts.
- Check that the Results saved item in Activities pops up
- Check that the new image(s) are imported with the associated regions to the chosen location.
- Check that also the other image which was already stored in OMERO has the new regions now associated to it in OMERO.
- close all images and ROI Manager in ImageJ
Recognizing the image which was freshly uploaded to OMERO.
- Open an image from your local drive in imageJ
- Use``Save Image(s) to OMERO`` to save the image into OMERO.
- Draw a ROI on the image and add it to ROI Manager in ImageJ.
- Click Save ROIs to OMERO.
- Check that the dialog indicating that the image is not imported does not pop up.
- Check that the ROI you just drawn is added to the previously imported image.
Using Save ROIs to OMERO to upload non-saved images as well.
- Open at least two images stored in OMERO in ImageJ using the imageJ plugin
- draw ROIs on both images and add them to Overlay (use Alt + B)
- select Plugins > Save ROIs to OMERO
- Check that a dialog Save ImageJ Results pops up [InsightIJI007d]
- select in a row both Save image from current window and Save image from all open windows radio button options
- select Save in the dialog and Check that the regions are now saved in OMERO as chosen in the dialog
- Draw a ROI and add it to the ROI Manager in ImageJ
- crop the image (draw a rectangle encompassing the region you have just drawn and select Image > Crop)
- select “Save ROIs to OMERO” item in Plugins > OMERO
- Check that the image is imported as ome-tiff WITH the region you have drawn on it.
- close all images and ROI Manager in ImageJ
Draw a ROI specifically on a z or t plane.
- open a multi-z and multi-t image stored in OMERO in ImageJ using the ImageJ plugin
- draw several ROIs (including an ellipse) in ImageJ on a particular z/t plane(s) and add them to ROI Manager in ImageJ (Note that Overlay in ImageJ does not support t information, but does support the z information.)
- also open test_images_good/tiff/QA images/Artificial_xyt_8bit.tif and draw several ROIs (including ellipse) in IJ on a particular plane and add them to Overlay (Ctrl + B)
- save the ROI using Save ROIs to OMERO on both images
- Check that the ROI in OMERO is associated with the correct z/t plane(s)
- in ImageJ, go to ROI Manager > More > Options and tick the Associate Show All... box
- restart ImageJ
- in OMERO, prepare another image with ROIs associated to different z/t planes
- open the image you prepared from OMERO in ImageJ using the plugin, ticking the options Display Metadata, Display OME-XML Metadata and Display ROIs options in the Bio-formats import options dialog and
- Check that now the ROI is associated to a particular z and t plane(s) in ImageJ and these plane(s) correspond with the plane(s) in OMERO
- Check the OME-XML to see if the newly added ROI’s have the correct Z,C and T information.

example of OME-XML with Z, C and T information:

<ROI ID="ROI:0:0" xmlns="http://www.openmicroscopy.org/Schemas/ROI/2015-01">
<Union>
<Shape ID="Shape:0:0" StrokeColor="-1" Text="0611-0860" TheC="1" TheT="1" TheZ="1">
<Rectangle Height="390.0" Width="780.0" X="470.0" Y="416.0"/>
<ROI ID="ROI:1:0" xmlns="http://www.openmicroscopy.org/Schemas/ROI/2015-01">
<Union>
<Shape ID="Shape:1:0" Text="1162-2035" TheC="1" TheT="1" TheZ="1">
<Rectangle Height="584.0" Width="250.0" X="1910.0" Y="870.0"/>

Testing Save Results to OMERO feature
- open an image from OMERO in ImageJ, draw an ROI and add to ROI Manager of IJ
- go to Analyze > Measure
- select Plugins > Save Results to OMERO
- Check that a dialog Save ImageJ Results pops up [InsightIJI007d]
- input a <name> for the .csv file to save (do not use periods in the name)
- Check that the Results saved item in Activities pops up
- Check that the csv file with the name <name>.csv is attached to the image in OMERO
- Check that when you leave the box for the name empty, the file is named ImageJ-<NameOfImage>-Results-<Date>.csv
Using Save Results to OMERO to upload non-saved images as well.
- Repeat the steps above with an image opened from your local disk
- Check that the image is imported and the measurements saved as <name>.csv file.
Open and save workflows for images
- open a z-stack image from OMERO in ImageJ
- open another z-stack image from OMERO in ImageJ
- go in IJ Image > Stacks > Tools > Concatenate...
- Upload and Save to OMERO the resulting image
- Check that the concatenated image has been imported successfully
MIF workflows
- in ImageJ, using Bio-Formats Importer, open test_images_good/leica-liff/Beta Catenin.lif
- select Select All in the popup window and click OK
- 5 images should be open
- draw a region on 3 of the images, adding it to Overlay every time
- use Save image(s) to OMERO to upload the MIF and ROIs to OMERO
- select in a row Add images from current window and Add images from All open window to test both workflows
- Check that in both cases, you have the whole MIF imported 1x with each ROI associated with the image you have drawn it on in ImageJ

Fiji

Start Fiji
Go Help > Update Fiji -> the update process will start. Restart Fiji and
- Check that you have the last release version of Bio-formats. To check the Bio-Formats version, go Help > About Plugins > LOCI Plugins [InsightIJI004]. Note that this does not have to be matching version with the OMERO version, as Bio-formats are decoupled from OMERO.
Add the OMERO.insight-ij* plugin to the Plugins folder of Fiji - on Mac, use rigth-click on Fiji icon & Show package content [InsightIJI003] to get to Plugins
Restart Fiji
Go Plugins > OMERO > Connect to OMERO
- Check that Insight splashscreen is displayed.
Log in.
Go to the left-hand pane and select an image or import one if no images available.
Double-click on the image and then click OK in the Bio-Formats Import Options window [InsightIJI006].
- Check that the image opens in Fiji.

Note that during the update, there might be a problem with the class org.joda.time.Instant which can be found here:

/Applications/Fiji.app/jars/jruby.jar
/Applications/Fiji.app/jars/loci_tools.jar
/Applications/Fiji.app/plugins/OMERO.insight-ij-5.0.0-rc1-ice35-b10/libs/joda-time.jar

The warning looks as follows:

WARNING: multiple locations found! java.lang.NoSuchMethodError: org.joda.time.Instant.parse(Ljava/lang/String;Lorg/joda/time/format/DateTimeFormatter;)Lorg/joda/time/Instant;

Solution: Delete the jruby.jar.