Filter

Core Feature

This feature is available in all MATISSE Explorer deployments.

The Filter allows you to build filter queries by combining multiple conditions with logical operators. This powerful tool enables precise data selection based on annotations, lasso selections, and variable sets.

Opening the Filter

Access the Filter from the Explorer view:

1. Click the Filter button in the map viewer toolbar
2. The Filter Panel opens

Filter Structure

Filters use a hierarchical structure:

Filter
├── Group 1
│   ├── Condition A  ─┬─ AND/OR
│   ├── Condition B  ─┤
│   └── Condition C  ─┘
│
├── AND/OR (group operator)
│
└── Group 2
    ├── Condition D  ─┬─ AND/OR
    └── Condition E  ─┘

• Conditions - Individual filter rules
• Groups - Collections of conditions combined with AND/OR
• Group Operator - Combines multiple groups with AND/OR

Condition Types

Column Condition

Filter by annotation values from your dataset.

For Categorical Columns:

• Select one or more categories to include
• Points matching any selected category pass the filter

For Continuous Columns:

• Set a value range or comparison
• Available operators:

  Operator	Meaning	Example
  Range	min ≤ value ≤ max	Expression between 0.5 and 2.0
  >	Greater than	Expression > 1.0
  ≥	Greater or equal	Expression ≥ 1.0
  <	Less than	Expression < 0.5
  ≤	Less or equal	Expression ≤ 0.5

Lasso Condition

Filter by saved lasso selections.

Lasso conditions are created by:

1. Drawing a lasso selection on the map or scatter plot
2. Clicking "Add selection to filter"

Each lasso condition includes:

• Name - Descriptive name (auto-generated or custom)
• Source - Where it was drawn (Spatial, UMAP, t-SNE, or Scatter Plot)
• Polygon - The boundary coordinates (stored internally)

Variable Set Condition

Filter by computed variable set scores.

Configure:

• Variable Set - Select from your created variable sets
• Combination Method - How to compute the score

  Method	Description
  Max	Maximum value across variables
  Min	Minimum value across variables
  Sum	Sum of all variable values
  Avg	Average of all variable values
  UMI Count	Normalized: ln(10000 × sum/totalUMI + 1)

• Comparison - Range or comparison operator with threshold

Creating Conditions

Add a New Condition

1. Click Add Condition within a group
2. Select the condition type (Column, Lasso, or Variable Set)
3. Configure the condition parameters
4. The filter updates preview automatically

Configure Column Condition

1. Click the column selector dropdown
2. Choose an annotation column
3. For categorical: select categories from the list
4. For continuous: set operator and value(s)

Configure Lasso Condition

Lasso conditions are added from the map viewer:

1. Draw a lasso selection
2. Click "Add selection to filter" from the Items dropdown
3. The lasso appears as a condition in the filter editor

Configure Variable Set Condition

1. Select a variable set from the dropdown
2. Choose the combination method
3. Set the comparison operator and value

Working with Groups

Add a New Group

1. Click Add Group at the filter level
2. A new empty group appears
3. Add conditions to the group

Set Group Operator

Choose how conditions within a group combine:

• AND - All conditions must match (intersection)
• OR - Any condition can match (union)

Set Filter Group Operator

Choose how multiple groups combine:

• AND - Points must match all groups
• OR - Points can match any group

Logical Operators Explained

AND Logic

Condition A AND Condition B

Result: Only points that satisfy both conditions

Example: Cell type = "T cell" AND CD3E > 1.0 → Shows only T cells with high CD3E expression

OR Logic

Condition A OR Condition B

Result: Points that satisfy either or both conditions

Example: Cell type = "T cell" OR Cell type = "NK cell" → Shows all T cells and NK cells

Combining Groups

(A AND B) OR (C AND D)

Result: Points matching Group 1 OR points matching Group 2

Example:

• Group 1: Region A AND high expression
• Group 2: Region B AND low expression → Shows high expressors in Region A plus low expressors in Region B

Managing Conditions

Edit a Condition

Click on any condition parameter to modify it:

• Change the column/variable set selection
• Adjust values or operators
• The filter recalculates automatically

Remove a Condition

1. Locate the condition to remove
2. Click the X or delete button
3. The condition is removed from the group

Remove a Group

1. Remove all conditions from the group, or
2. Click the group's delete button
3. The entire group is removed

Applying Filters

Preview

As you build your filter, the map view updates to show matching points. The point count indicates how many items pass the filter.

Apply

Click Apply to confirm and apply the filter. The filtered view becomes active.

Clear

Click Clear or remove all conditions to reset the filter and show all points.

Complex Filter Examples

Example 1: Specific Cell Type in Region

Goal: Find B cells in a specific tissue region

Group 1 (AND):
├── Column: cell_type = "B cell"
└── Lasso: "Germinal Center" (spatial selection)

Example 2: High Expression of Gene Set

Goal: Find cells highly expressing immune genes

Group 1 (AND):
├── Variable Set: "Immune Markers" (Max)
└── Comparison: > 2.0

Example 3: Multiple Regions Comparison

Goal: Compare two tissue regions

Filter (OR):
├── Group 1 (AND):
│   ├── Lasso: "Region A"
│   └── Column: n_genes > 1000
│
└── Group 2 (AND):
    ├── Lasso: "Region B"
    └── Column: n_genes > 1000

Tips and Best Practices

1. Start simple - Begin with one condition, then add complexity
2. Use preview - Check results as you build the filter
3. Name lasso selections - Use descriptive names for saved regions
4. Save presets - Store frequently used filters for reuse
5. Consider performance - Very complex filters may take longer to compute

Troubleshooting

No Points Match

• Check if conditions are too restrictive
• Verify AND logic isn't excluding everything
• Try relaxing value ranges

Unexpected Results

• Review the logical operators (AND vs OR)
• Check group operator setting
• Verify column values are correct

Filter Not Updating

• Ensure changes are applied
• Check for loading indicators
• Refresh if necessary

Related Topics

• Lasso Selection - Creating lasso conditions
• Filter Presets - Saving and loading filters
• Variable Sets - Creating variable sets