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Manual Version
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Software Version
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Date
|
Description
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|---|---|---|---|
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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
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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
|
V5.5.3
|
Mar. 2023
|
Improvement: upgrade
mapping pipeline module, which performs polyA filtering after CID
mapping, for improved statistical output in report.
|
|
A6
|
V6.0
|
Mar. 2023
|
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.
|
|
A7 |
A6.2 | Jul. 2023 |
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
Improvement: updated |
|
A8
|
V7.0
|
Oct. 2023
|
New feature:
supported H&E image in pipeline; addition of
Improvement: performance
improvement in
count and |