v7.1

• New feature: addition of Proteomics &Transcriptomics jointly analysis required modules, including mapping-SP,calibration, spatialCluster-SP,cellCluster-SP,multiomicsAnalysis and report-PT; supported Proteomics mode in modules: tissueCut and cellCut; addition of new small tools: MIDFilter, which supported extract GEF based on MID range.

v7.0

• New feature: supported H&E image in pipeline; addition of cellCorrect module for expanding cell boundaries; addition of cellChunk module for displaying cell expression heatmap in StereoMap; addition of a new parameter in spatialCluster for adjusting Leiden clustering resolution; addition of output GEF file in lasso module.
• Improvement: performance improvement in count and register modules; updated tissue and cell segmentation model for nuclei-staining image; supported for using GPU in register module to accelerate computing.

v6.1

• New feature: supported outputs of Valid ClD Reads and un-mapped reads in FASTQ format; supported QC-failed but manually processed images as inputs for subsequent workflow; addition of tissue area (nm²) in corresponding GEF file; supported generating GEF file of labeled region; addition of quality control alerts and tissue segmentation display in report.
• Improvement: updated mapping module to improve computational efficiency; updated the error alerts on checking the length of the gene name, in checkGTF and count modules.

v6.0.0

• New Feature: addition of rRNAremove switch in mapping, off 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 continuously processing image files output from each module of ImageStudio.
• Improvement: reconstructed tissueCut module pipeline, with the addition of parameter -t which means the number of used CPUs, to greatly improve the calculation efficiency; modified parameter -g in img2rpi module to a two-layer structure, upgraded RPI file format to support storing and organizing multiple stained microscopy images in groups; displayed pseudo colors (up to 7 colors) on the bottom layer of clustering results in HTML report, when handling the scenario of mIF in report module.
• Bug Fix: fix the bug caused by version compatibility when generating CGEF file.

v5.5.0

• 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.

v5.4.0

• 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;