ReCognize
User Guide

Revision 2022-11-30-63359ec
How to ...
Options : default | deep | row | grid | random

Options : box selection | free-hand selection | circle selection

Index
Launch ReCognize

You can launch the ReCognize application from the Filemanager on the portal. The filemanager can be found in the menu Data & Analysis (in section headed Data Management), and the menu entry is called Molecular Cartography Data.

Every dataset (row) that is ready for visualization will have a green 3D button (see below) in the column labeled Action on the right. A red icon indicates that the dataset is still being prepared and not yet ready for visualization. An example of a dataset ready for visualization is shown below.

Gene panel

Search box
Search and find gene names
Color Picker
To defind the color of gene by picking a color or enter a value.
Quick toggle
Toggle shown / hidden genes
Quick visual switching
| Show all genes
| Hide all genes
| Show only genes assigned to groups
| Select genes by expression range
Gene Layout
| Layout
  • default
  • Grid showcase
| Layout Config
  • Number in a row
  • font-size
  • Image shows behind
Distance Tool
Measure the distance between transcripts
Gene config
| Camera Position
  • Z position value in µm unit
  • Distance information - The distance from the camera to the tissue.
  • Coordinate information - The position of the camera.
| Scale type
  • Scale bar - from 50 µm to 5000 µm.
  • Size (Width & Height)
  • Position the scale bar by clicking
| Point size - adjust transcript size.
| Z dimension scale - Select the scaling of transcript Z coordinate values.
| Rotating speed - Set the rotation speed during your coffee break
| Color running speed - Set the color change frequency during your coffee break
Quick group name generator
Create the gene group name and dop-drag the name to the box behind the expression name. It's done by assigning a group name to a single gene.
Sort gene list by name.
Sort gene list by expression counts.
Sort gene list by group names.

Gene panel | Color set
Save color and group settings of your gene list for later use. Enter a name and click to save. Click on a color set name to load a previously saved set. To export the currently selected set as JSON file, click . These files can be shared and imported by clicking the button. To permanently delete the currently selected color set, click .
Feature panels
Features
Screen Shot
Rotation
X - flip
Y - flip
/ Dimension mode
Control Zoom in/out
Feature | ROIS & Cluster
ROIS
ROIS files
Select the ROI set to be loaded. ROIs sets can be added to a dataset as supporting data in the file upload section of our portal.
Style
ROI polygon style, plane or line.
Opacity
Set transparency level of ROI polygons.
Z-Position
Set the Z position of ROI polygons.
Load selected ROI set.
Show / Hide
ROI colors
Loaded ROIs are either shown in white or in the corresponding color of the cluster after performing a cell type clustering. Here you can colorize loaded ROIs according to their gene expression. You can select up to three genes and assign them to either R(ed), G(reen) or B(lue). The color of each ROI is mixed from the three primary colors in proportion to the transcript counts of selected genes. To return to the default coloring, remove genes from the color selection menu.
Cluster
Cell type clustering based on gene expression patterns. We use the Seurat package for analysis with the following commands:
This feature requires a loaded ROI set of segmented cells. Please upload a corresponding support data file in advance.

Start the cell type clustering calculation
Jump to clustering results.

Filtering Parameters
Filter Genes Min Cells Filter genes by the minimum number of cells/ROIs expressing it
range:1 - 500
Filter Cells Min Features Filter cells by minimum number of different genes expressed
range:1 - 50
Min Transcripts Filter cells by minimum total number of transcripts
range:1 - 100
Clustering Parameters Dimension Number of PCA dimensions
Resolution Clustering Resolution
Genes Use only currently selected genes
Download cluster result

Press this button to download a zip file with the results of the latest celltype clustering. The zip file contains:

  • The raw transcript counts per gene/cell matrix
  • The counts matrix after applying filter settings, used for the clustering
  • The parameters used for the clustering
  • The assignement of cell IDs to cluster IDs
  • A list of average gene expressions per cluster
  • A list of informative marker genes per cluster
  • A 2d UMAP plot
  • The gene expression heatmap
  • The exported Seurat object that can be imported into a local R session





    • Feature | UMAP plot
    This panel shows the UMAP representation of ROIs in 3D. Each spot in this plot represents an ROI in the loaded ROI set. The location of spots relative to each other relates to their similarity in gene expression profile. This panel can be used to select spots in UMAP space to highlight their location in spatial context to quickly compare functional and spatial relationships.

    Rotation start / stop
    Default
    Rotation and pan the plot.
    Box selection
    Click and drag in the UMAP plot to make a box selection of ROIs.
    Free-hand selection
    Click and drag to make a free-hand selection of ROIs.

    Panel Size
    Large
    Meddle
    Small
    Back to section

    ROI colors
    Colorize ROIs according to their gene expression. See also ROI colors section above .
    Feature | Region Transcript Counter
    This feature allows to select areas in the main panel and to count the number of transcripts per gene contained in each region. Counts per region or total counts over all selected regions will be displayed as bar plots. Counts can also be exported as CSV file for further analysis.

    Box selection
    Click and drag in the main window to make a box selection. The selected region will be automatically added to the region list.

    Free-hand selection
    Draw a region freely on the transcript in which you prefer to observe the details.

    Selection results.
    Selects this region to be displayed in the bar chart above. The x axis can be sorted by gene name or transcript count value in ascending or descending order
    Show / hide selection in main window.

    Delete selection.

    Show total counts of all regions in bar chart.

    Export count data of all selections as CSV file.



    The panel is expendable so genes with proper sapce displaying
    Feature | Image
    Load microscope images to be displayed in the background, such as DAPI staining or bright-field images. To use this feature, please upload a corresponding jpeg or png file as supporting data in the upload section of our portal.

    Image
    Select image file to be displayed.
    Z-position
    Adjust z-position of image.
    Opacity
    Set transparency level of image.
    Feature | Capture
    This feature allows to capture the main window panel and export the content as video file.

    start recording.

    recording and download video file.
    Screen Shot
    Launch the screen shot tool

    Main Image
    Select window panel to be captured
    --- Tissue & Cluster (default)
    --- UMAP
    --- Heatmap
    Legend
    Customize gene legend
    --- Invisible
    --- All genes, highlight selected (default)
    --- Groups only
    --- All genes, groups highlighted
    --- Clusters names
    --- Clusters names and genes
    Genes per column
    --- 60
    --- 50
    --- 40 (default)
    --- 30
    --- 20
    --- 10
    Group per column
    --- 8
    --- 7
    --- 6 (default)
    --- 5
    --- 4
    --- 3
    --- 2
    --- 1
    Legend background
    --- large (default)
    --- medium
    --- small
    --- hidden
    File Name
    --- Specify file name.
    Image size
    --- Default (default)
    --- Medium
    --- Small
    --- x-small
    Image Resolution
    --- 8K (7680px x 4320px)
    --- 4K (3840px x 2160px)(default)
    --- 2K (2048px x 1080px)
    Preview mode
    Check this box to display the location of the image border in the main window for precise arrangement of final shot.
    Image Type
    --- PNG (default)
    --- JPG
    --- Tiff
    Platform logo
    --- Visible (default)
    --- Invisible
    Company logo
    --- Visible (default)
    --- Invisible

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