Version description

SAW operation manual

Version description

Revision History

Manual Version	Software Version	Date	Description
A0	V1.0.0	Nov. 2021	Initial release.
A1	V2.1.0	Dec. 2021	New feature: addition of manual registration function, some fine-tuning will be automatically performed after manually registering; Improvement: performance improvement for mapping; the order of sequencing saturation calculation has switched, in v2.1.0 we only compute the saturation of tissue-covered region; Bug fix: fix the bug of indexing at mapping step; fix the bug of long waiting time at register step.
A1.1	V2.1.0	Jan. 2022	Add error handling; Update demo output
A2	V4.1.0	Apr. 2022	New feature: support to process fused microscopic images; employ Stereopy in clustering; new gene expression matrix file format; including a file format convertor and a mapping memory estimator; Improvement: performance improvement for mapping; update gene annotation approach in count; update image stitching and tissue segmentation model for better performance on image stitching and segmentation for tissue with voids.
A3	V5.1.3	Aug. 2022	New feature: addition of cell segmentation on microscopic image in register pipeline module and cellCut pipeline module to extract cell expression matrix; design IPR file to store image processing record information and TIFF images produced in register; output exon expression matrix along with total MID count; addition of cell clustering analysis; addition of cell bin statistic result and image information in HTML report; add pipeline modules to support single-end FASTQ data; addition of option for selecting multi-mapped reads; addition of score system in image processing; Improvement: addition of poly A filtration in mapping; performance improvement for merge, tissueCut and saturation; add data scaling and upgrade clustering analysis pipeline; Bug fix: fix the bug of plotting scatter plot in tissueCut, review and modify the ambiguous metrics names and explanations in HTML report;
A3.1	V5.1.3	Dec. 2022	Bug fix: fix the typo in the manual.
A4	V5.4.0	Nov. 2022	New feature: render a more elegant way of organizing SE FASTQs input into mapping; addition of header for count output TXT file; upgrade ipr2img to imageTools which allows you to merge TIFF images to check segmentation result and plot templates on the panoramic image or registered image to check the result of stitching and registration; Improvement: change data struct of gene index in the GEF file from uint16 to uint32 to store more genes; Bug fix: fix the typo in the manual;
A5	V5.5.0-V5.5.2	Jan. 2023	New feature: addition of manualRegister and lasso pipeline modules, which acquire parameters and essential files from offline visualization software StereoMap; addition of error code function in each module, and the explanation has been organized in appendix D; Improvement: upgrade tissueCut pipeline module for better performance and improved accuracy of tissue recognition directly from gene expression matrix; upgrade clustering analysis pipelines; addition of image layers in HTML report which allow users to switch images displayed with gene expression distribution plot; the stitching deviation heatmap(s) and the frame of axes in the HTML report have been adjusted according to the registration parameters.
A5.1	V5.5.3	Mar. 2023	Improvement: upgrade mapping pipeline module, which performs polyA filtering after CID mapping, for improved statistical output in report.

Note: Please download the latest version of the manual and use it with the software specific to this manual.

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