Support & Documentation

MantaPlex currently supports single-cell and spatial phenotyping of 2-dimensional immunofluorescent tissue images, for lowplex to highplex panels.

MantaPlex converts all images to Zarr internally for optimal performance.

• OME-Zarr (.zarr): Highly recommended. It completely bypasses the conversion step for faster importing and includes full v0.5 metadata support.
• Zeiss CZI (.czi): Fully supported with complete metadata retention.
• TIFF (.tiff, .tif): Supported, but metadata compatibility varies by variant (see below).

Supported TIFF Variants: While MantaPlex easily reads raw pixel data, proprietary TIFF metadata structures vary widely. We strictly support the following variants:

• OME-TIFF (.ome.tiff, .ome.tif): The recommended TIFF variant. Offers full metadata support.
• QPTIFF (.qptiff, .qptif): Fully supported with complete metadata.
• Leica SCN (.scn): Fully supported with complete metadata.
• ImageJ (.tiff, .tif): Supported with best-effort metadata parsing.

Not at the moment.

There is currently no known limit to image file size; MantaPlex has been internally validated with images up to 200GB.

Yes, MantaPlex can import polygons which are in geojson format.

Operating system requirements- minimum: Windows 10, recommended: Windows 11. System requirements - Minimum: RAM 8GB, CPU: 2 cores @2.5GHz, Disk: 1 GB free (application only), recommended: RAM 16GB, CPU: 8+ cores @4GHz, Disk: SSD with 100+ GB for your data (as needed). You will need an Intel Core processor or any AMD processor manufactured after 2011.

For unsupported formats or compatibility questions, please contact us at contact@mantalys.fr . If you need to import unsupported data, you can convert it beforehand using third-party tools like QuPath, bioformats2raw, or ImageJ. We highly recommend using QuPath (the easiest and most versatile option) to export your data to OME-Zarr for optimal compatibility.

There is currently no known limit to channel number; it has been internally validated with 30+ channels. The image viewer limits the number of channels that can be simultaneously to six; the number of channels that can be viewed individually in the Grid View is unlimited.

You are welcome to check out our video tutorials and our troubleshooting documentation for pertinent fixes to common problems. If you encounter a bug, you can use the bug report feature directly in the app or reach out to us at contact@mantalys.fr for support with the software.

MantaPlex currently offers nuclear dilation but our upcoming version will support additional algorithms for direct cell segmentation.

Please check our system requirements to ensure that your workstation meets the specifications. If you use an old CPU, you might need to install the old CPU-compatible version. Please contact us to receive a link to download the old CPU-compatible version of MantaPlex.
Please note that MantaPlex automatically performs a file conversion step which generates a duplicate image file with a .zarr extension for optimal performance. Large files may take longer to process. This conversion step will fail if there is insufficient space on your disk.

To adjust the parameters for nuclear segmentation, click on the Parameters icon of the Cell Segmentation module within the Single-Cell Analysis pipeline. Here you can try different segmentation models, modify the thresholding method, and exclude nuclei beyond a specific size range.
Two types of thresholding methods are offered for the nuclear channel: either automatic thresholding, which utilizes Median Absolute Deviation, or manual thresholding, which uses the low slider in the Analysis profile of the Channels tab to set the threshold.

If you are unsatisfied with the automatically generated tissue mask, you have three options:
(i) you can preview different parameters for the automatic tissue mask generation until you achieve satisfactory results (ii) you can edit the vertices of the existing tissue mask, or (iii) you may delete the automatically generated mask entirely and draw one using our polygon draw tool.

Check the Supported File Types document to ensure your file type is supported. Check that all images in the project are configured with the same number of channels.
If you need to import unsupported file types, you can convert them beforehand using third-party tools like QuPath, bioformats2raw, or ImageJ. We highly recommend using QuPath (the easiest and most versatile option) to export your data to OME-Zarr for optimal compatibility.

Clustering and classification results depend upon thresholds specified for each channel in the "Analysis" channel profile. Any signal below the low threshold is considered background noise and excluded during normalization. After adjusting the low threshold of your channel of interest in the “Analysis” channel profile, be sure to save and apply the results to the whole cohort.

To see if the bug resolves immediately, press Ctrl + R to refresh the page. If the problem persists, you can use the “Report a Bug” feature in the app. To access this, click on the envelope icon in the top navigation bar and fill the required information. Screenshots and logs are helpful to our team in isolating the source of the problem.