# Release Notes ## Release Notes for SAW ### 8.2.2 (Dec., 2025) **Bug fixes:** * 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. *** ### 8.2.1 (Nov., 2025) **New feature:** * SAW count/realign * `--skip-clustering` enables skipping the step related to clustering analysis in the workflow; **Bug fixes:** * 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. * Fixed numerical precision issues in the statistical table under the Protein-SquareBin tab of the HTML report. * Fixed an error that occurred when the `--gpu-id` was set to a non-zero GPU index. *** ### 8.2.0 (Sep., 2025) **New feature:** * SAW makeRef * Support `--params-config` to directly input the original command lines of third-party bioinformatical tools. * 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](/saw-user-manual-v8.2/advanced/parallel-computing.md#parallel-alignment-of-fastqs) for multiple paired/grouped FASTQ files during read alignment, to improve resource utilization and runtime efficiency. * `--description` can customize the remarks of the analysis, displayed in the HTML report. * `--skip-cellbin` helps skip image-based cell segmentation and related analysis steps. * `--no-bam` can remove the output annotated BAM file, reducing storage usage. * `--create-gem` can output corresponding expression matrices in GEM format. * `--summary-display-bin-size` supports effectively displaying the analysis results within the summary tabs of each omics category, chosen from \[20,50,100], * `--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 `--gpu-id` option for image processing. * `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. * 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). **Upgrade:** * SAW checkGTF * Optimized the inspection and format modification of annotation files. * SAW makeRef * Automatically invokes `checkGTF` to inspect annotation files when building STAR index files. * SAW count/realign * Optimized analysis of RNA filtering based on specific adapter sequences, to improve the fraction of Confidently Mapped Reads. * Optimized performance of the read annotation, particularly when the `--uniquely-mapped-only` and `--rRNA-remove` options are enabled. * Read annotation has improved the inspection and format checking of annotation files (GTF/GFF), automatically bypassing problematic annotation records. * Even for an image that failed image QC, the analysis will still output the matrix template file in `visualization.tar.gz`. * 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 * Optimize the calculation of L2FC values for genes in differential expression analysis. * SAW convert * Optimize the logic for directly generating the cellbin GEM file, in `bin2cell`. * Optimized log formats and content for the analysis pipeline and sub-programs. * Enhanced error codes with more detailed and explicit error messages. * Removed unnecessary intermediate output files to reduce storage redundancy. * Addition of `_statistics.json` file to provide comprehensive statistics for the entire analysis pipeline. **Bug fixes:** * Fixed an issue where the program encountered an exception when processing large image data (BigTIFF format files), primarily affecting large Stereo-seq chip datasets. *** ### 8.1.3 (Mar., 2025) **Bug fixes:** * Fixed the issue that parameters `--bin-size` and `--resolution` in `SAW reanalyze cluster` did not take effect for proteomics data. * Fixed the saving issue of processing large chip data in `SAW convert overlay`. * Fixed the issue that GPU failed to work in `SAW count` and `realign` due to the dependency installation problems. * Fixed the issue of abnormal exit when `--image` file path contains "czi" in `SAW count`. * Fixed the issue of abonormal exit when the image ROI is less than (2000,2000) in `SAW count` and `realign`. * Fixed the issue that HTML report cannot be opened for large chip data, by downsampling bin20. clustering plot and UMAP plot. Fixed the display problem of saturation plot. Fixed the description issue of protein correlation heatmap. **Upgrade:** * Stereo-seq N FFPE V1.0 `--sequencing-type` supports `PE75_25+59` and `PE75_25+62` (new). * Supported annotation file suffixed with `.gff3` in `SAW count`. * Supported Bowtie2 large index file suffix with `.bt2l` in `SAW count`. * Upgraded cell segmentation in H\&E image for fresh frozen sample. *** ### 8.1.2 (Nov., 2024) **Bug fixes:** * Prompt exception, when `--adt-fastqs ` files are corrupted. **Upgrade:** * `SAW count` and `realign` output HTML report as `.report.html` , and you can open it directly. All plots can be downloaded. * Reduce memory usage in `SAW count` Annotation. * 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. * Accept FASTQ files named as `*_R1.fq.gz` and `*_R2.fq.gz`. * Support the prefix of transcriptome reference index directory as `STAR`. Compatible with `STAR_SJ100` built by previous SAW 6.1\~7.1. * Improve input validation, including the validity of file or directory paths in `--ref-libraries `; the validity of file paths of image TIFF or TAR.GZ; and check the format of protein panels. * 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`. *** ### 8.1.1 (Oct., 2024) **Bug fixes:** * `SAW realign` * Fixed the issue that QC-failed images could not run normally after manual processing. * Fixed the abnormal call of built-in quality control information in the HTML report. * Output the Microorganism expression matrix to `visualization.tar.gz`. * Fixed the problem that the Microorganism `micro` module has no permission to access the file from `SAW count`. * `SAW reanalyze` * Fixed the problem that the parameter `--Leiden-resolution` is not effective, in `SAW reanalyze cluster` cellbin mode. * Solved the problem of `numpy` library query error caused by conflict between user local python environment and SAW built-in python environment. **Upgrade:** * Supports `--image` TIFF images as soft links with [correct naming specifications](/saw-user-manual-v8.2/analysis/pipelines/saw-commands.md#saw-count). *** ### 8.1.0 (Sep., 2024) **New feature:** * Stereo-CITE FF samples is available in SAW released as a self-contained `tar.gz` file. It is implemented by setting `--kit-version` to `"Stereo-CITE T FF V1.x"`, when running `SAW count`. SAW v8.1.0 or later is needed for Stereo-CITE FF analysis. * Support `Stereo-seq FF kit=V1.3` by setting `--kit-version` to `"Stereo-seq T FF V1.3"`when running `SAW count`. * `SAW reanalyze` * `midFilter` Performe manually filtering spatial expression matrices by MID range. * `multiomics` Proteome & Transcriptome joint analysis. * `removeBackground` Automatic protein background removal. **Upgrade:** * `SAW reanalyze` is called by submodules, and you can use functions like: * `SAW reanalyze lasso` * Upgraded the bioinformatical workflow * Defaultly cutting adapters in `SAW count` alignment, instead of directly discarding reads with adapter. * Clustering in bin GEF mode omits zero-centering variables to handle sparse input. * Adjusted marker selection thresholds in Proteome & Transcriptome joint analysis. * Upgraded the HTML report from `SAW count` and `SAW realign`. Page Square Bin can display bin20 and bin50 clustering and UMAP projection. * The compressed image `.tar.gz` file completed by feature point registration from StereoMap, can be accpeted by `--image-tar`. SAW v8.1.0 or later is needed for feature point registration. * Fixed the appearance of cells with large single area after cell segmentation. **Bug fixes:** * Fixed several known issues. *** ### 8.0.2 (Jul., 2024) **Bug fixes:** * Fixed several known issues. *** ### 8.0.1 (Jul., 2024) **Bug fixes:** * Fixed serveral known issues. *** ### 8.0.0 (Jun., 2024) **New form:** 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. Because it has assembled all of the software-required dependencies, which are pre-compiled to run on most Linux distributions. **New feature:** * 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 Kit 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. More in [Preparation of reference](/saw-user-manual-v8.2/tutorials/preparation-of-reference.md). * Upgraded the bioinformatical workflow of read alignment and annotation, which adapts to FFPE datasets. * 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. * As for the image-related part, the software has optimized the image processing performance. Meanwhile, the microscope-stitched image, in TIFF, is supported as input directly when running `SAW count`. * 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. * The diagrams in the HTML report are interactive. The microorganism analysis page and the marker feature result table are added to the HTML report. * Reorganized output directory structure to make result files much clearer, and intermediate files and logs into designated folders. * Output the packaged `visualization.tar.gz` file, which includes `.stereo` file, containing SAW pipeline analysis information and records needed by StereoMap. ### Previous ones Release information for earlier versions can also be found on our [Software Archives](https://en.stomics.tech/resources/software-archives.html) and [GitHub](https://github.com/STOmics/SAW). *** **Access to help** Have any questions or concerns about SAW versions? Please get in touch with the **local agents** or **FAS/FBS**. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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