|
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
|
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 |
