# SAW

{% hint style="success" %}
SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics. *Gigabyte.* <https://doi.org/10.46471/gigabyte.111>
{% endhint %}

## SAW 8.2.2 (Dec., 2025)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.2.2.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  8.1 G</td><td>md5: 53473c7f46581c1bc088e6e6d57d8b20</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.2.2.tar.gz "https://enfile.stomics.tech/saw-8.2.2.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.2.2.tar.gz "https://enfile.stomics.tech/saw-8.2.2.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.2.2 highlights:

* Fixed an issue where the statistics within tissue area under the Microbe tab of the HTML report, generated by SAW realign, failed to update automatically. The report now recalculates these statistics based on the new segmentation region (e.g., manual tissue segmentation).
* Fixed a calculation error affecting Q30 values in the output statistical JSON file when processing multiple pairs of FASTQ files.
* Fixed an incorrect default sorting order of images in the HTML report when displaying DAPI + mIF results.

***

## SAW 8.2.1 (Nov., 2025)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.2.1.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  8.1 G</td><td>md5: 87dd7c28dcb5387d0ba3f29b9c609a99</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.2.1.tar.gz "https://enfile.stomics.tech/saw-8.2.1.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.2.1.tar.gz "https://enfile.stomics.tech/saw-8.2.1.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.2.1 highlights:

* SAW count/realign
  * `--skip-clustering` enables skipping the step related to clustering analysis in the workflow;
* Fixed an error caused during the process of microorganism detection, due to NFS-mounted disks on the server.
* Fixed an error in the image processing module when handling the microscope image TIFF from Stereo-seq 0.5\*0.5 chips.
* Fixed the data overflow error encountered in GEF matrix files when processing extremely large datasets generated by large-sized Stereo-seq chips.

***

## SAW 8.2.0 (Sep., 2025)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.2.0.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  8.1 G</td><td>md5: a286749d0f172bd0dfa632f37df89a89</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.2.0.tar.gz "https://enfile.stomics.tech/saw-8.2.0.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.2.0.tar.gz "https://enfile.stomics.tech/saw-8.2.0.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.2.0 highlights:

* SAW makeRef
  * Support `--params-config` to directly input the original command lines of third-party bioinformatical tools.
  * Automatically invokes `checkGTF` to inspect annotation files when building STAR index files.
* SAW count/realign
  * Supports data analysis for Stereo-seq N FFPE V1.1 kit, with new analysis parameters:
    * `--kit-version="Stereo-seq N FFPE V1.1"`
    * `--sequencing-type=PE75_50+100`
  * Read alignment supports parallel computation for multiple paired/grouped FASTQ files during read alignment, to improve resource utilization and runtime efficiency.
  * Optimized analysis of RNA filtering based on specific adapter sequences, to improve the fraction of Confidently Mapped Reads.
  * `--skip-cellbin` helps skip image-based cell segmentation and related analysis steps.
  * `--summary-display-bin-size` supports effectively displaying the analysis results within the summary tabs of each omics category, chosen from \[20,50,100],&#x20;
  * `--custom-bin-size` allows custom bin sizes within the analysis pipeline. It is mainly used for secondary analysis and report presentation.
  * Introduced the Initial Check function to inspect formats of the main input datasets and software integrity before starting the analysis, with `--no-initial-check` to disable it.
  * `--job-mode` supports SGE cluster analysis, or a specific resource-configuration yaml file, enabling more refined and in-depth resource scheduling.
  * `realign` now supports `--extra-image-enhance` to set additional passes of CLAHE-based image enhancement that are applied following the default image processing. The image enhanced by this parameter is utilized for cell segmentation.
  * HTML report
    * Upgraded the UI design of the report interface, primarily including color schemes and page layouts.
    * The report content display logic has been upgraded, with the navigation bar organized according to a multimodal/multi-omics perspective. Field descriptions and explanations have been updated, and the sample information chart and the image registration check module have been added.
    * In the Microbe page, the metrics have been adjusted to display information specific to the detected tissue region.
    * In the Summary tab, the `--summary-display-bin-size` option is used to adjust the bin size for data display.

      In the Square Bin tab, the `--custom-bin-size` option is used to adjust the bin size of downstream analysis for result display.
    * In the Cell Bin tab, the cell area unit in the statistical table has been changed from pixels to μm².
    * In the ​​Square Bin and Cell Bin tabs, the report enables downsampling functionality for clustering and UMAP visualizations for large Stereo-seq chips (those with too many points during plotting).
* SAW reanalyze
  * Support spatial gene co-expression analysis.
* SAW convert
  * Support outputting RDS files for analysis in Seurat, by `gef2rds`, `gem2rds` and `h5ad2rds`.
  * `bin2tissue` can extract expression matrices based on tissue segmentation maps, and also support tissue segmentation directly based on a gene expression matrix (without images).
* Optimized log formats and content for the analysis pipeline and sub-programs.
* Enhanced error codes with more detailed and explicit error messages.
* Addition of `<SN>_statistics.json` file to provide comprehensive statistics for the entire analysis pipeline.

***

## SAW 8.1.3 (Mar., 2025)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.1.3.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  5.7G</td><td>md5: 6cd872cffcf539a8c3a2e5447bc290cd</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.1.3.tar.gz "https://enfile.stomics.tech/saw-8.1.3.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.1.3.tar.gz "https://enfile.stomics.tech/saw-8.1.3.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.1.3 highlights:

* Stereo-seq N FFPE V1.0 `--sequencing-type` supports `PE75_25+59` and `PE75_25+62`.
* Reduce HTML report file size for large chip data and downsample bin20 clustering and UMAP plots.
* Upgrade cell segmentation in H\&E image for fresh frozen sample.

## SAW 8.1.2 (Nov., 2024)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.1.2.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  7.6G</td><td>md5: 9a895f3364d4e0cd5faaaaa909e4d3eb</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.1.2.tar.gz "https://enfile.stomics.tech/saw-8.1.2.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.1.2.tar.gz "https://enfile.stomics.tech/saw-8.1.2.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.1.2 highlights:

* `SAW count` and `realign` output HTML report as `<SN>.report.html` , and you can open it directly. All plots can be downloaded.
* Reduce memory usage in `SAW count` Annotation.&#x20;
* Upgrade totalVI model. Proteome & Transcriptome joint analysis, this module will not be executed in the `SAW count` and `realign` . You can use this analysis in `SAW reanalyze multiomics` .
* Improve tissue segmentation based on the image.
* Support the prefix of transcriptome reference index directory as `STAR`. Compatible with `STAR_SJ100` built by previous SAW 6.1\~7.1.
* Cell bin GEF from `SAW convert` and `reanalyze`, can be visualized directly in **StereoMap**.
* Change bin GEF attribute /wholeExp/maxMID to 100% max MID numbers, instead of 99.9%. Reduce the file size of output bin GEF in `SAW reanalyze lasso`.&#x20;

## SAW 8.1.1 (Oct., 2024)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.1.1.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  5.6G</td><td>md5: 52aa36786d4fb0504455447414a8b060</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.1.1.tar.gz "https://enfile.stomics.tech/saw-8.1.1.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.1.1.tar.gz "https://enfile.stomics.tech/saw-8.1.1.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.1.1 highlights:

* Output the Microorganism expression matrix to `visualization.tar.gz`.
* `--image` supports accepting TIFF images in soft link format, when performing `SAW count`.
* Fixed the issue that SAW could not handle the registration of QC-failed image and the expression matrix after manual processing.
* Fixed the problem that the parameter `--Leiden-resolution` is not correctly passed, in `SAW reanalyze cluster` cellbin mode.

## SAW 8.1.0 (Sep., 2024)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.1.0.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size:  5.6G</td><td>md5: bce4e53952350970ceb416503801f4dd</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.1.0.tar.gz "https://enfile.stomics.tech/saw-8.1.0.tar.gz"
```

{% endtab %}

{% tab title="wget" %}
{% code overflow="wrap" %}

```bash
wget -O saw-8.1.0.tar.gz "https://enfile.stomics.tech/saw-8.1.0.tar.gz"
```

{% endcode %}
{% endtab %}
{% endtabs %}

SAW 8.1.0 highlights:

* SAW now supports running analysis pipelines with data from new STOmics kit products, `Stereo-CITE FF V1.0` and `Stereo-seq FF V1.3`.
* SAW has introduced new submodules under `SAW reanalyze`, `midFilter` for manually filtering spatial expression matrices by MID range, `multiomics` for Proteome & Transcriptome joint analysis, `removeBackground` for automatic protein background removal.
* `SAW count` alignment now trims adapter sequences, and filters the remaining fragments by length limit when handling RNA reads, instead of directly discarding them, more in \[Algorithms/Read processing algorithms].
* `--image-tar` of `SAW count` can accept the compressed image `.tar.gz` which is completed by feature point registration from StereoMap. SAW v8.1.0 or later is needed for feature point registration.
* HTML report displays both bin20 and bin50 clustering and UMAP projection.

## SAW 8.0.2 (Jul., 2024)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.0.2.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size: 3.0 GB</td><td>md5: 0ca72ea8d7a990fdcf0ff88063ad2f77</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}
{% code overflow="wrap" %}

```bash
curl -o saw-8.0.2.tar.gz "https://enfile.stomics.tech/saw-8.0.2.tar.gz"
```

{% endcode %}
{% endtab %}

{% tab title="wget" %}

```bash
wget -O saw-8.0.2.tar.gz "https://enfile.stomics.tech/saw-8.0.2.tar.gz"
```

{% endtab %}
{% endtabs %}

SAW 8.0.2 highlights:

* Optimized the memory usage during the annotation of RNA reads.&#x20;
* Optimized the memory usage of gefpy when executing the lasso function.&#x20;
* Fixed the issue that the tissueCut program could not process large chip image data (bigTIFF, exceeding 4GB).&#x20;

## SAW 8.0.1 (Jun., 2024)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw_8.0.1.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size: 3.0 GB</td><td>md5: afd82ed454f5ab06c8f24ff2572f10b9</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.0.1.tar.gz "https://enfile.stomics.tech/saw-8.0.1.tar.gz"
```

{% endtab %}

{% tab title="wget" %}

```bash
wget -O saw-8.0.1.tar.gz "https://enfile.stomics.tech/saw-8.0.1.tar.gz"
```

{% endtab %}
{% endtabs %}

SAW 8.0.1 highlights:

* Corrected the indicator calculation instructions of the Tissue part under the Summary tab of the HTML report, and cancelled the hover display of the heatmap under the Microorganism tab.
* Fixed the error when running `SAW realign` analysis after the original path of the `SAW count` output result was changed.
* Fixed the error when `SAW reanalyze` performed clustering analysis on bin GEF files.
* Removed redundant temporary files generated by the annotation programming module.

## SAW 8.0.0 (Jun., 2024)

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th></tr></thead><tbody><tr><td><a href="https://enfile.stomics.tech/saw-8.0.0.tar.gz"><strong>Download for Linux 64-bit (tar.gz)</strong></a></td><td></td></tr><tr><td>File size: 3.0 GB</td><td>md5: bce3798c227276f6cbe19af6b1bacdae</td></tr></tbody></table>

{% tabs %}
{% tab title="curl" %}

```bash
curl -o saw-8.0.0.tar.gz "https://enfile.stomics.tech/saw-8.0.0.tar.gz"
```

{% endtab %}

{% tab title="wget" %}

```bash
wget -O saw-8.0.0.tar.gz "https://enfile.stomics.tech/saw-8.0.0.tar.gz"
```

{% endtab %}
{% endtabs %}

SAW 8.0.0 highlights:

* SAW is released as a self-contained `tar.gz` file that can be unpacked directly on the system, without the need to configure the computing environment.&#x20;
* Integrated and simplified pipelines facilitate inputting command lines and complete analysis. \
  The pipelines include:
  * `SAW count`: the main pipeline to count gene expression reads and generate expression matrices from the Stereo-seq chip
    * `SAW makeRef`: prepare index files of the reference data
    * `SAW checkGTF`: check the annotation file format
    * `SAW realign`: restart analysis with manually processed files
    * `SAW reanalyze`: perform secondary analysis
    * `SAW convert`: support file format conversions
* Gene expression from FFPE (formalin-fixed paraffin-embedded) samples is available in SAW, and is implemented by setting `--kit-version` to `"Stereo-seq N FFPE V1.0"`, when running `SAW count`. SAW v8.0.0 or later is needed for FFPE analysis.
* Microorganism analysis can be switched on when perform `SAW count` run based on Stereo-seq FFPE tissue sample, by using `--microorganism-detect`. You have to prepare indispensable references for it.
* Upgraded the bioinformatical workflow of read alignment and annotation, which adapts to FFPE datasets.&#x20;
  * During annotation, uniquely mapped reads and the best match among multi-mapped reads are used together by default. If the analyst focuses only on uniquely mapped reads, `--uniquely-mapped-only` will be helpful.
  * New spatial gene expression matrices are identified by unique gene ID, and record gene ID and name.
* Differential expression analysis is added to SAW analysis, which is performed based on Leiden clustering. Marker features are recorded both in AnnData H5AD and CSV, and displayed in HTML report and StereoMap.
* Output the packaged `visualization.tar.gz` file, which includes `.stereo` file, containing SAW pipeline analysis information and records needed by StereoMap.

***

## SAW < 8.0

SAW versions earlier than 8.0 were published on dockerhub. Only stable versions of each major release are kept.

Visit SAW dockerhub repository: <https://hub.docker.com/repository/docker/stomics/saw/tags>

### SAW 7.1.2 (Jul., 2024)

{% tabs %}
{% tab title="docker" %}

```bash
docker pull stomics/saw:07.1.2
```

{% endtab %}

{% tab title="singularity" %}

```bash
singularity build SAW_7.1.sif docker://stomics/saw:07.1.2
```

{% endtab %}
{% endtabs %}

SAW 7.1.0-7.1.2 highlights:

* New feature:&#x20;
  * addition of Proteomics & Transcriptomics jointly analysis required modules, including `mapping-SP`, `calibration`, `spatialCluster-SP`, `cellCluster-SP`, `multiomicsAnalysis` and `report-PT`.
  * supported Proteomics mode in `tissueCut` and `cellCut`.
  * addtion of a new small tools, `MIDFilter`, which supported extract GEF based on MID range.
* Bug fix:
  * for `multiomicsAnalysis`, removed duplicated gene names in marker genes plot;&#x20;
  * for `report-PT`, fixed Page 'Image' not visible when image exists;
  * for wholeExp layer in visual GEF, fixed invalid data type of MIDCount when bin size > 1;&#x20;
  * for `lasso`, fixed extraction in cellbin GEF does not match interested area.

***

## End of Support

The following software versions have reached **End of Support** status. We will no longer provide technical support, bug fixes, feature updates, documentation updates, or compatibility assurance. While your current software may continue to function, we strongly recommend upgrading to the latest version. New versions are fully compatible with all Stereo-seq kits and designed to meet current demands.&#x20;

### SAW 7.0.1 (Feb., 2024)

{% tabs %}
{% tab title="docker" %}

```bash
docker pull stomics/saw:07.0.1
```

{% endtab %}

{% tab title="singularity" %}

```bash
singularity build SAW_7.0.sif docker://stomics/saw:07.0.1
```

{% endtab %}
{% endtabs %}

SAW 7.0.0-7.0.1 highlights:

* New feature:&#x20;
  * supported H\&E image in pipeline;&#x20;
  * addition of `cellCorrect` module for expanding cell boundaries;&#x20;
  * addition of new parameter in `spatialCluster` for adjusting Leiden clustering resolution;&#x20;
  * addition of output GEF file in `lasso` module.
* Improvement:&#x20;
  * performance improvement in `count` module;
  * performance improvement in `register` module, supported for using GPU in `register` module to accelerate computing.
  * updated tissue and cell segmentation model for nuclei-stain image;&#x20;

### SAW 6.1.4 (Mar., 2024)

{% tabs %}
{% tab title="docker" %}

```bash
docker pull stomics/saw:06.1.4
```

{% endtab %}

{% tab title="singularity" %}

```bash
singularity build SAW_6.1.sif docker://stomics/saw:06.1.4
```

{% endtab %}
{% endtabs %}

SAW 6.1.0-6.1.4 highlights:

* New feature:&#x20;
  * support outputs of `Valid ClD Reads` and `Un-mapped Reads` in FASTQ format.&#x20;
  * support QC-failed but manually processed images as inputs for subsequent workflow.&#x20;
  * addition of tissue area (nm²) in the corresponding GEF file.
  * support generating GEF file of the labeled region in `lasso`.&#x20;
  * addition of quality control alerts and tissue segmentation display in HTML report.
* Improvement:&#x20;
  * updated `mapping` module to improve computational efficiency, you need to make a new reference index, refer to <https://github.com/STOmics/SAW/tree/v6.1/Scripts/pre_buildIndexedRef>.
  * updated the error alerts on checking the length of the gene name, in `checkGTF` and `count` modules.
* Bug fix:&#x20;
  * for `tissueCut`, corrected the statistical method of `Reads_under_tissue` item in `tissueCut`, which now represents "Number of reads with position prior to filtration under tissue coverage"
  * for `report`, fixed matrix heatmap missing for QC-failed .ipr file
  * for`manualRegister` module, fixed an error in calculating the offset due to incorrect selection of the scaling direction
  * for `manualRegister`, fixed the problem that obtaining image width and height incorrectly from StereoMap manual registration JSON file
  * for `imgeTool`, fixed the problem that manually registered images were incorrectly cropped after scale operation
  * for `report`, fixed the missing percentage value of the floating text box for 'Sequencing Saturation' in HTML

### SAW 6.0.2 (May, 2023)

{% tabs %}
{% tab title="docker" %}

```bash
docker pull stomics/saw:06.0.2
```

{% endtab %}

{% tab title="singularity" %}

```bash
singularity build SAW_6.0.sif docker://stomics/saw:06.0.2
```

{% endtab %}
{% endtabs %}

SAW 6.0.0-6.0.2 highlights:

* New feature:&#x20;
  * addition of `rRNAremove` switch in `mapping`, disable by default, to count and filter rRNA reads using the reference genome with the addition of rRNA information. rRNA count and ratio are recorded in the output file.
  * support the scenario with the combination of DAPI and mIF (multiple immunofluorescence images), correspondingly generating registered, tissue segmentation, and cell segmentation results.
  * support processing image files output from each module of ImageStudio.
* Improvement:&#x20;
  * reconstructed `tissueCut` module and improve the calculation efficiency.
* Bug fix:&#x20;
  * fixed the bug that the execution path of `checkGTF` function was invalid.&#x20;
  * for `register`, fixed the issue that the module was unable to get `.czi` file path.
  * fixed the trackline template acquisition error.&#x20;

### SAW 5.5.4 (Apr., 2023)

{% tabs %}
{% tab title="docker" %}

```bash
docker pull stomics/saw:05.5.4
```

{% endtab %}

{% tab title="singularity" %}

```bash
singularity build SAW_5.5.sif docker://stomics/saw:05.5.4
```

{% endtab %}
{% endtabs %}

SAW 5.5.0-5.5.4 highlights:

* New feature:&#x20;
  * addition of `manualRegister` and `lasso` modules, which acquire parameters and essential files from StereoMap.
  * addition of error code function in each module, and the explanation has been organized in appendix D.
* Improvement:&#x20;
  * upgraded `mapping` module, which performs polyA filtering after CID mapping.
  * upgraded `tissueCut` module for better performance, improved accuracy of tissue recognition directly from gene expression matrix.
  * upgraded clustering analysis.
  * addition of image layers in HTML report which allow users to switch images displayed with gene expression.
* Bug fix:&#x20;
  * fixed the execution path of `checkGTF` was invalid.

### SAW 5.4.0 (Nov., 2022)

{% tabs %}
{% tab title="docker" %}

```bash
docker pull stomics/saw:05.4.0
```

{% endtab %}

{% tab title="singularity" %}

```bash
singularity build SAW_5.4.sif docker://stomics/saw:05.4.0
```

{% endtab %}
{% endtabs %}

SAW 5.4.0 highlights:

* New feature:&#x20;
  * a new way of organizing Q4 FASTQs input into analysis.
  * addition of header for the output TXT file of `count` module.
  * upgraded `imageTools` to allows merging TIFF images to check segmentation result, and support plotting templates on the panoramic image or registered image to check the result of stitching and registration.