CSV Export

Core Feature

This feature is available in all MATISSE Explorer deployments.

Export annotation data to CSV format for use in external analysis tools, spreadsheets, or archiving.

Accessing CSV Export

CSV export is available from the Explorer sidebar. Each annotation column has a download button that provides export options.

1. Open the Explorer extension
2. In the Annotations tab, find the column you want to export
3. Click the Download icon (↓) next to the column name
4. Select an export option from the dropdown menu

Export Options

When you click the download button, a dropdown menu appears with two options:

Download All Data

Exports the complete dataset for the selected column, regardless of any active filters.

Download Selected Data

Exports only the data points that pass your current filter. This option is:

• Enabled when a filter is active
• Disabled (grayed out) when no filter is applied

TIP

Use "Download selected data" to export specific subsets of your data after applying filters or lasso selections.

Supported Column Types

Categorical Columns

Exports category labels for each data point.

Output format:

index,cell_type
AAACCCAAGAAACACT-1,B cell
AAACCCAAGAAACTGT-1,T cell
AAACCCAAGAAAGACA-1,T cell
AAACCCAAGAAAGGCT-1,Macrophage
...

Continuous Columns

Exports numeric values (e.g., gene expression) for each data point.

Output format:

index,CD3E
AAACCCAAGAAACACT-1,0.0
AAACCCAAGAAACTGT-1,2.345
AAACCCAAGAAAGACA-1,1.892
AAACCCAAGAAAGGCT-1,0.0
...

Embedding Columns

Exports X and Y coordinates from projection data (e.g., UMAP, t-SNE, spatial coordinates).

Output format:

index,UMAP x,UMAP y
AAACCCAAGAAACACT-1,1.234,5.678
AAACCCAAGAAACTGT-1,2.345,6.789
AAACCCAAGAAAGACA-1,-0.123,4.567
...

File Details

File Naming

Exported files are automatically named based on the column:

• {column_name}.csv

Examples:

• cell_type.csv
• CD3E.csv
• UMAP.csv

Index Column

The first column (index) contains:

• Cell/observation IDs if an ID column is configured in the dataset
• Numeric indices (0, 1, 2, ...) if no ID column is available

Encoding

• UTF-8 encoding
• Standard CSV comma delimiters
• Values containing commas, quotes, or newlines are properly escaped

Working with Exported Data

In Excel

1. Double-click the CSV file to open directly, or
2. Use Data > From Text/CSV for more import options
3. Verify columns are detected correctly

In R

data <- read.csv("cell_type.csv")
head(data)

In Python

import pandas as pd
data = pd.read_csv("cell_type.csv")
data.head()

Large Dataset Handling

CSV export uses streaming technology to handle large datasets efficiently:

• Files download progressively as they are generated
• No file size limit imposed by the browser
• Memory-efficient for datasets with millions of points

WARNING

For very large exports, ensure you have sufficient disk space and a stable internet connection.

DEG Analysis Results Export

InSilicoLab Feature

DEG result export is exclusive to Portrai InSilicoLab.

Differential expression analysis results can be exported from the DEG Analysis workspace. See DEG Analysis - Data Table CSV Export for details.

Troubleshooting

Download Button Not Responding

• Ensure the annotation data is fully loaded (no loading spinner)
• Try refreshing the page

"Download Selected Data" is Disabled

• This option requires an active filter
• Apply a filter or lasso selection first

File Contains Fewer Rows Than Expected

• Check if "Download selected data" was used instead of "Download all data"
• Verify your filter settings

Download Interrupted

• Check your internet connection
• Ensure sufficient disk space
• Try downloading again

Related Topics

• Image Export - Export visualizations as PNG images
• Annotations - Understanding annotation types
• Filter - Filter data before export
• DEG Analysis - DEG results CSV export