> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-stratamap/references/software-release-notes.md).

# Software Release Notes

## June 2026

{% hint style="warning" %}
Use only 'v2' software versions together. The software has switched to the term 'slide ID' instead of 'substrate ID', which means files from ISIT v1.1 will not be compatible with v2.0 secondary analysis without manual adjustment.
{% endhint %}

#### Illumina Spatial Image Tool v2.1.4

* Homepage re-design: deprecated ‘Microscope Assessment’ workflow, added demo data, log-in connectivity check, disk space check, and easy access to log files.
* Expanded image compatibility: Multi-sample support from single image (to support slide scanner images), larger image size, and additional supported file types: QPTIFF, PNG, ND2, SVS.
* Automatic pixel size detection 
* Redesign of image QC to simplify assessment of quality, including filters of warnings. More helpful text on meaning of results and possible next steps.
* Tissue masking improvements: Addition of product type (Large slide, 6-well slide, Small slide) with warning when tissue is outside the active area of specified product.

#### DRAGEN Spatial Transcriptome v2.0.0

* Report re-design: added run diagnostics, wadditional statistics and metrics, and the ability to access separate per-sample report pages.
* Improved speed and memory usage.
* v3 cell segmentation model: provides improved nuclei detection accuracy for better cell identification. Cell segmentation now also provides ROI (region of interest) Previews to enable quicker visual evaluation of segmentation results.
* Imageless analysis available. When images are unavailable the software can still be run providing grid-binned data only.
* Multimapping enabled by default: more reads are captured by including those mapping to multiple genes, improving sensitivity.
* Re-designed Results folder structure: cleaner organization with MTX files in the Results folder and a ready-to-import ICM (Illumina Connected Multiomics) package.
* Coordinates in microns: Results data now reported in microns for easier interpretation and compatibility with downstream tools.
* Local version available as a DAM (DRAGEN Application Manager) app on a v4 DRAGEN Server. Contact your Illumina support representative if you are interested in this option.

## November 2025

{% hint style="warning" %}
Use only v1.1 software versions together. The Illumina Spatial Image Tool generates OME-TIFF files with filenames that differ from those in v1.0, making them incompatible with v1.0 DRAGEN Spatial Transcriptome secondary analysis without manual adjustment.
{% endhint %}

#### Illumina Spatial Image Tool v1.1

* General usability updates
  * Updated button actions
  * Retain history of logs where log file is renamed from main.log to YYYY-MM-DD.log​
  * Abort immediately upon clicking of Cancel button during any process (Registration of Image, Generation of OME TIFF)​
* Updates to QC
  * Added pixel metadata check
  * Updated messages
  * More robust rotation check
* Tissue masking updates
  * Tooltips on icons
  * New mask color for improved visibility
  * Ability to view selected buffer before completing the review
  * Ability to remove and add back in areas
  * Zoom in/out while editing
* Added more logging
* Fixed export bugs: timeout error and export support for different regions

#### DRAGEN Spatial Transcriptome v1.1

* Multiple performance improvements
* Large sample support: increased to support larger samples
  * Tissue area - up to 433 mm2
  * Sequencing depth - up to 5x 25B
* Custom genome support (non-human/mouse species)
* Cell segmentation
  * Updated cell segmentation model
  * Standalone cell-segmentation pipeline
  * Optional nuclei binning


---

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