48. ROI Insight

To test in: Insight

Purpose of the test is to check main ROI features in Insight (creation, editing, propagation, merging, result collection and export)

Section 1: Create ROI, Manager, Inspector and Results tabs

  1. Open an image with multiple z/t planes in Full Viewer

  2. Open ROI tool

    • from the icon on the top of the Full Viewer [ROIInsight001:]

    • from the main menu go Controls > ROI Tool

  3. Create ROIs (more than 3) of different types including Text (Text is one of ROI types).[ROIInsight002:]

  4. Use a multi-t image.

    • Create ROI and project it across all time points

    • Delete the ROI

    • Create new ROI, project across all time points

    • Close Viewer

    • Save changes when prompted

    • Check that the new ROI IS saved

  5. Draw a line and “break” into segments and Save

    • Go to the Results tab.

    • The length should display length per segment and the total. Same for angle.

    • Export to Excel. The value displayed in table should be exported as such in Excel.

  6. Add comment to the shape (double-click on the shape and write). Tick and untick the Show comment box

    • Check that the comment appears and disappears.[ROIInsight003]

    • Check that when the only action after the image was open was toggling the Show comment box, no dialog asking whether you want to save pops up

  7. Create a Text ROI (the A icon in ROI manager).

    • Check that changes in the color of the text are displayed instantly, not just after you saved the text ROI.

  8. Select and de-select the ROIs and shapes. Check that type is correct and it corresponds with the selection in Viewer.

  9. Move shapes and close the full viewer.

    • Check that dialog asking whether you want to save pops up.

  10. Propagate shapes, Merge shapes from different z or t planes, Split shapes (which you Merged previously), Duplicate and Delete shapes [ROIInsight005][ROIInsight006:][ROIInsight007:, ROIInsight008]. Execute these 5 commands from

    • right-click menu on the region in the image

    • right-click menu on the ROI in the list in Measurement Tools window

  11. Change Fill and Line color [ROIInsight009:]. Change width and height of a shape (Inspector tab).

    • Check the changes of the region display.

  12. In Results tab, add new Measurements and remove Measurements using Results wizard.

    • Click on a row, check that the chosen region/plane changes in the image.

    • Export to Excel.

    • Check the file was created.

  13. Units

    • Import test_images_good/EM-data/

    • Draw a line region

    • Check that the units and values in the Results tab are correctly displayed. This means checking in the General Tab the size of the pixel and judge from it how long approximately your line should be and compare it with what is displayed.

  14. Select a Big image

    • Check that only Manager, Inspector and Results tabs are displayed in the ROI Tool and columns are populated.

    • Check that the area is now displayed when drawing a rectangle for example.

    • Check that the font size changes according to the resolution level.

Section 2: Graph, Intensity View and Intensity Results View tabs:

  1. Choose a region propagated on more than 2 z and 2 t planes & scroll through the histograms

  2. Choose a Line-type of region.

    • Check that both Line profile and Histogram are shown.

    • Export the graph as JPEG or PNG. Only the line plot should be exported.

    • Check that when you hover over the line in the Graph, in case the pixel size of the image is known, it shows the tooltip with current position in microns.

  3. Repeat the step 2 but this time with a rectangle. Note that no Line profile will be shown in this case.

  4. In Graph Tab, progress through T using both the slider in the ROI tool and in the Full Viewer of the image.
    • Close the ROI tool.

    • Go through T in the Full Viewer of the image.

    • Check that the ROI tool window does not reopen.

    • Check that no other unexpected windows pop up (such as magnifying tool).

    • Check that the Help menu of the image is not empty.

  5. Try to create new regions when on Graph pane and to propagate them

    • Using the magic wand icon

    • Using right-click on the region

    • Check: message appears “ROI assistant cannot be used in graph pane or intensity view”.

  6. Switch channels on/off on the image. Select different regions. Scroll through z planes on the Graph tab

    • Check that the graphs update

    • Check that the planes in the stack of images updates concurrently

    • Turn channels on off. Check that histogram updates.

  7. In Intensity View tab:

    • Check that when no region is selected, the Intensity Values button is greyed out.

    • Select a region in the image which you have saved before.

    • Click to Intensity Values button.

    • Check that window pops up with intensity values of single pixels [ROIInsight009b:].

    • Toggle channels on the image on/off.

    • Change the channel selection in the Intensity Values window.

    • Export to Excel.

    • Check the file.

    • Close the image viewer, reopen it and open the ROI tool again.

  8. Intensity Results View tab.

  9. Check freeze at low memory does not occur.

    • Reduce the default memory allocated to insight

      • right-click on Insight and click on Show package contents

      • edit the info.plist file

      • note down what are the settings from around Line 110 of this file of <string>-Xms&&M -Xmx&&M</string> (note down the numbers replaced here by &&)

      • change these settings to <string>-Xms64M -Xmx64M</string>

    • Draw a rectangle and propagate the shape across few z or t

    • Select the shape

    • Go to “Intensity Results Tab” and add the selected shape

    • After a while, a dialog indicating that an error occurred will pop up.

    • Click OK and check that all the controls do not stay greyed out.

    • Set the default memory allocated to Insight back to the same value as it was before you reduced it.

  10. Multi-t/z addition behaviour check

    • Draw a line and propagate it across z or t.

    • Select the shape

    • Go to “Intensity Results Tab” and add the selected shape

    • Wait till the results of the shapes composing the ROI are displayed in the table.

    • Scroll to a new plane where the shape has been propagated. Check that the results of the shapes composing the ROI are not added again to the table.

    • Draw another line. Save. Select and Add it. Make sure that only rows corresponding to the new line are added.

  11. Add selected test1

    • Go away from Intensity Results View tab (i.e. select Manager tab).

    • Still NOT being on Intensity Results View tab, select one region to add (in Results/Manager tabs or in the image itself)

    • NOW Select Intensity Results View tab (the region is still selected - do not change your selection now)

    • Press Add Selected

    • Check the data were added to the table [ROIInsight010:]

    • Try to select more regions and press Add Selected

    • Check the data were added to the table [ROIInsight010:]

    • Try Remove and Remove All buttons.

    • Add data again and Export to Excel

    • Check the file. [ROIInsight011]

  12. Add selected test2

    • Draw a rectangle for example.

    • Go the Intensity View Tab. Wait till the results are displayed.

    • Go the Intensity Results View Tab, Click Add selected. the results should be displayed.

Section 3: ROIs created in 3rd party software

  1. 3rd Party ROIs:

    • Import all the files from data_repo/test_images_good/zeiss-lsm/roi-scenario

    • Import all the files from data_repo/test_images_roi/zvi/

    • All the images thus imported should have ROIs on them.

    • Open all the images.

    • Check that the ROIs are displayed.

  2. Shapes without linkage to a plane

    • Create a shape (a ROI) not linked to any plane, for example in ImageJ (see Insight as Plugin ImageJ/Fiji , Section ImageJ - ROI and OMERO upload, step 1 for instructions).

    • Import the image into OMERO using OMERO.insight, NOT the IJ-plugin.

    • Open the image in Insight, open the Measurement Tool, do not save the ROI

    • Go to the Graph, Intensity View, Intensity Result View.

    • Check that the shape is analysed.

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