# View tissue images * [Visualize the annotated image from the automatically generated Spatial report task](#visualize-the-annotated-image-from-the-automatically-generated-spatial-report-task) * [Visualize the annotated image from the Annotate Visium image task](#visualize-the-annotated-image-from-the-annotate-visium-image-task) * [Modify Style](#modify-style) * [Modify Axes](#modify-axes) * [Color by gene expression and attributes](#color-by-gene-expression-and-attributes) ## Visualize the annotated image from the automatically generated Spatial report task [With the pre-processed samples imported, we can begin analysis.](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/start-with-pre-processed-space-ranger-output-files) * Click **Analyses** to switch to the *Analyses* tab For now, the *Analyses* tab has a starting node, a circular node called *Single cell* counts and also a rectangular task node called *Spatial report* which was automatically generated for this type of data. As you [perform analyses, additional nodes representing tasks and new data will be created](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/spatial-data-analysis-steps), forming a visual representation of your analysis pipeline. * Click the **Spatial report** node * Click **Task report** on the task menu ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-df83095239cbfde4cf675641824b0f19152122f8%2Fimage2023-12-11_17-29-5.png?alt=media) The spatial report will display the first sample (Replicate 1). We want to visualize all of the samples using the steps below. * Duplicate the plot by clicking the **Duplicate plot** button in the upper right controls (arrow 1) * Open the **Axes** configuration option (arrow 2) * Change the Sample on the duplicated image under *Misc* (arrow 3) ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-0ba9b16955b4595ef20648ec19c41b9ec8a680a9%2Fimage2023-12-11_17-40-40.png?alt=media) Each data point is a tissue spot. Duplicate and change the sample to view multiple samples. ## Visualize the annotated image from the Annotate Visium image task If starting with unprocessed [fastq files](https://github.com/illumina-swi/partek-docs/blob/main/docs/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/start-with-10x-genomics-visium-fastq-files/README.md), the *Annotate Visium image* task will create a new result node, *Annotated counts*. * Double click on the **Annotated counts** node to invoke the *Data Viewer* showing data points overlaid on top of the microscopy image * Follow the steps outlined above by duplicating the image to visualize the multiple samples ## Modify Style To modify the points on the image to show more of the background image use the Style configuration option. * Press and hold Ctrl or Shift to select both plots * Click **Style** in the left panel * Move the *Opacity* slider to the left * Change the *Point size* to 3 ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d88593c48cffe4bf192cb440d481a25978e68ea3%2Fimage2023-12-11_17-46-4.png?alt=media) * Click **Save** in the left panel and give the session an appropriate name ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-5c1500baa32a4b218595de1191807df5b337d987%2Fimage2023-12-11_19-29-42.png?alt=media) ## Modify Axes Modify the axes to remove the X and Y coordinates from the tissue image. * Press and hold Ctrl or Shift to select both plots * Click **Axes** in the left panel * Toggle off *Show lines* for both the X & Y axis * Toggle off *Show title* and *Show axis* for both the X & Y axis ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-7fe0c53ece0d2c235486b1af24575b891142f6a0%2Fimage2023-12-11_19-32-3.png?alt=media) ## Color by gene expression and attributes Style the image and color by normalized gene expression using three genes of interest. * Press and hold Ctrl or Shift to select both plots * Click **Style** * Click the blue circle node ![image2023-12-12\_13-21-34](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-de43de5c6de9805a9dae865e93115dddb9318ed8%2Fblue-circle-node.png?alt=media) to the right of the *Color by* drop-down * Select the *Normalized counts* node as the source * Choose to **Color by** *Numeric triad* * Use the Green drop-down to select IL32, Red drop-down to select DES, and Blue drop-down to select PTGDS genes (type in name of gene in drop-down) * Increase the *Point size* to 11 ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9cd290689593a145b837fb397430126278591197%2Fimage2023-12-11_21-8-21.png?alt=media) To color by the [Cell attribute "Cell Type"](https://help.connected.illumina.com/partek/partek-flow/tutorials/spatial-data-analysis-steps#publish-cell-attributes-to-project) which we previously determined in this tutorial, use the **Color by** drop-down and select Cell Type. Cell type is a blue categorical attribute while green attributes are numerical. ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-1a9aa8b08738c56e7eb9cd434b6a2d0eb69be5e6%2Fimage2023-12-12_14-30-26.png?alt=media) ## Additional Assistance If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.