Create figures using OMERO.figure ================================= OMERO.figure is a web-based tool for creating figures from Images in OMERO. Image metadata can be used to facilitate figure creation. Description ----------- This guide covers: - Opening images in OMERO.figure to create a new figure - How to add additional images to an existing figure - Arranging panels in the desired figure layout - How to synchronize the rendering settings between panels - How to add scalebars, labels and ROIs to panels - How to save and export figures as PDF or TIFF Setup ----- - Install the OMERO.figure web app as described at https://pypi.org/project/omero-figure/ Resources --------- - Sample images from the Image Data Resource (IDR) `idr0021 `__. See `idr0021-data-prep.md `__ for download and import instructions. - DV images from `siRNAi-HeLa `__. - SVS ‘big’ pathology images from `SVS `__. Step-by-Step ------------ Using the sample images above, we will create a figure like this, but you can use any multi-channel images. .. image:: images/image0.png :align: center #. In the webclient, select 6 images from the **idr0021** Project. #. In the right-hand panel, click the *Open with...* button and choose *OMERO.figure*: .. image:: images/image1.png :scale: 75 % #. This will open these images in OMERO.figure in a new browser tab. #. Drag to arrange the Images approximately into two rows, select all (use Ctrl-A or drag to select) and click the *snap to grid* button |image2|\ at the top of the page. #. Select all Images and Zoom in around ~300%, using the Zoom slider in the right *Preview* tab. #. Go to the *Labels* tab, select all Images and add a Scalebar: Click the *Show* button, choose a length of 2 μm, click the *Label* checkbox and adjust the size of the Label to 12. #. Add labels: choose *Dataset Name* in the label input dropdown list, choose *color white* and *position=top-left*. .. image:: images/image3.png :scale: 75 % #. Click *Add* to create the new label. #. Add labels: choose *Key-Value Pairs* in the label input dropdown list, and in the following popup choose the Key which you want to add the value of from the dropdown menu. .. image:: images/image3a.png :scale: 75 % #. Click *OK* in that dialog to create the new label. #. Select one image. In the *Labels* tab, click the *Edit* button for ROIs. #. If the image has ROIs in OMERO, click *Load ROIs.* #. Mouse over the list to show each ROI on the Image and click to add it to the Image. #. Click *OK* to close the dialog. #. Return to the webclient tab, select the **siRNAi-HeLa** Dataset. N.B.: You may wish to filter the images when selecting those to add to your figure, e.g. Filter by Rating. #. Select 3 images and in the right-hand panel click the link icon |image4|\ then copy the link. #. Return to the OMERO.figure tab, click *Add Image* button and paste the link into dialog. Click OK. #. Arrange the 3 images into a vertical column, select all and click *snap to grid* button. #. Copy the 3 images and paste (keyboard shortcut or *Edit > Copy/Paste*) 3 times to create 3 more columns. #. Select the panels in the first column and adjust the rendering settings: Turn only the first channel on and set the color to white. #. Repeat for the next 2 columns: 1 channel turned on for each column, adjusting the levels if desired, leaving the 4th column as **merged** with multiple channels on. #. Select all panels and zoom a little. Then select all the panels from one row and drag the image in the *Preview* tab to pan the selected images to the same point. #. Copy and paste the **merged** column again to create a 5th column. Zoom in to approx 500%. #. Select the *Labels* tab, select the **merged** and **zoomed** columns and click *Show* Scalebar button. #. Click the *Label* checkbox to add a label to the scalebar. Select only the zoomed-in panels and change the scalebar to 1 micron. #. Select the top-left panel and enter a label text in the *Add Labels* form. “Prometaphase” in the example above. #. Set the label size (14), position (left vertical) and color (black) and click *Add* to create a label. #. If we have Tags on the images, we can use these to create labels: #. Select the first column of panels and choose *Tags* from the label text-field drop-down options. Click Add. #. Select the first row of panels and create the labels in the *top* position using the *Channels* option to add Labels for active channels in each image. #. Edit the created labels located at the bottom of the *Info* tab to rename the green labels to **GFP-INCENP**. #. Select just the first **merged** Image and click the ROIs *Edit* button in the *Labels* tab. #. Draw arrows or other shapes on the Image, or load ROIs from OMERO. Click *OK* to close the dialog. #. Click *Copy* ROIs in the *Labels* tab, select the other panels in the same row and click *Paste* to add ROIs to these panels. #. To create a Rectangle ROI indicating the region of the zoomed-in image, select the zoomed-in image on the first row and click *Copy* of the cropped region at the bottom of the *Preview* tab. #. Now select the zoomed-out **‘merged’** panel, and paste this region as an ROI by clicking *Paste* under ROIs section of the *Labels* tab. #. Repeat for other rows of the figure. At this point we have created the figure in the screenshot above. Saving and exporting figures ---------------------------- #. Go to *File* > *Paper Setup...* and in the dialog that pops up choose *Pages: 2.* Click *OK*. #. Finally return to the webclient, select ‘Big’ images from the **svs** Dataset, copy the link to them and paste it into the *Add Image* dialog in OMERO.figure. #. Move the big images to the 2nd page. #. In the header, click on the *Save* button to save the Figure as “Figure 1”. #. The URL will update. You can bookmark this URL or share with collaborators to view your figure. #. To open other saved files, go *File > Open...* #. We can view figures from our collaborators here and filter by name or Owner. #. Choose a figure to Open. For example the **Aurora-B figure 2** from trainer-2. #. Select a panel and click on the *Webclient* link in the *Info* tab to show the image in the webclient. #. Back in OMERO.figure, go to *File > Open...* to choose the “Figure 1” file saved above. #. Click on *Export PDF* to export it as PDF. #. Download the PDF and open it. If opened in a suitable application e.g. Illustrator, the elements on the page will still be editable. .. |image2| image:: images/image2.png :width: 0.20833in :height: 0.20833in .. |image4| image:: images/image4.png :width: 0.36458in :height: 0.25in