Release Notes

Release Notes for SAW

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 abnormal 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.

• Fixed the issue where the input QC-failed image TAR.GZ file was being deleted in SAW 8.1.2 count. Alternatively, the input image TAR.GZ can be found in visualization.tar.gz.

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 <FASTQ> files are corrupted.

Upgrade:

• 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.

• 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 <CSV>; 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.

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.

• Supported 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.

• 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 and GitHub.

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