5.2.7336.3219

• new simple workbench toolset for metabonomics data analysis and visualization
• new view GCxGC rawdata file
• new LC-MS reference spectrum library management
• enhancement make improvements of the 3d ms-imaging model viewer: allowes load raw raster byte volume model
• enhancement MoNA online services plugin for build local LCMS reference spectrum library
• fixed fix for load GCMS netCDF rawdata file(add new file reader based on the unidata netcdf-c library)
• update add supports of metabonomics data analysis for the selected interested ion layer in ms-imaging viewer

🎉🎇🎇2024
🎉Happy chinese new year!
🧨🧨🧨🎉🎉🎇🎇

What's Changed

• Ms1 deco math by @xieguigang in #24
• Oligonucleotide ms by @xieguigang in #25
• Update README.md by @xieguigang in #26

Full Changelog: 4.5.139.9689...5.2.7336.3219

get release download: https://cdn-biodeep-cn-obs.obs.cn-east-2.myhuaweicloud.com/tools/MZKit-20240209-Setup%20Files.zip

4.5.139.9689

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.

Downloads: http://www.biodeep.cn/downloads?lang=en-US

This is a release update edition for PANOMIX spatial metabolism
Wish you peace and health on Chinese Dragon Boat Festival!

• new Enable mzkit for imports 10x genomics raw data file for do slide sample imaging
• new Enable mzkit for do ms-imaging slide sample rotation, just use the button [Rotate Slide] in MSI operations menu.
• new Add ion annotation table imports for ms-imaging viewer, this function required a csv table that contains the target ions' m/z, name, formula, precursor_type information.
• enhancement show physical ruler overlap in the ms-imaging render, you can turn off this overlap by set showPhysicalRuler option to false
• enhancement show total ions ms-imaging overlaps in the ms-imaging render, you can turn off this overlap by set showTotalIonOverlap option to false
• enhancement enable adjust the ion polarity mode for the ms-imaging data viewer, this option value will affects some ion metabolite annotation related function in mzkit ms-imaging data viewer
• enhancement add more ms-imaging related properties to displayed in ms-imaging viewer: resolution, physical size in unit mm, file type, etc.
• enhancement enable imports custom ion layer in the ion layer selector of the ms-imaging viewer, data imports could be comes from a csv or xlsx table file.
• enhancement Add tweaks of the parameters when do ms-imaging row scan raw data file combines
• fixed fix of the possible bug in the background R# script data backend when create the ms-imaging heatmap matrix
• enhancement enable set the color palette when create the ms-imaging heatmap matrix, you can just tweaks of this parameter in the [Settings] tab page on the ms-imaging heatmap matrix editor
• new Add a color scaler bar besides the ms-imaging viewer, you can adjust the intensity scaler range manually via this color scaler bar. This color scaler bar not working for the RGB ms-imaging render.
• new View ion m/z distribution histogram in ms-imaging viewer. You can found this option in [MSI Analysis] -> [Feature Detections] menu.
• new Add umap manifold + dbscan clustering for do slide sample auto-segmentation
• enhancement Now the umap 3d scatter viewer could interactive with the ms-imaging viewer: you can select the ms-imaging pixel spot via mouse click on the scatter point in umap 3d scatter viewer
• enhancement Enable the ms-imaging viewer imports the umap cluster dataset as the sample slide segmentation data source
• enhancement Add scatter size options for tweaks the point size when view the tissue segmentation result overlap with the ms-imaging
• update removes the biodeep login condition for the targetted metabolism data handler
• enhancement make improvements of the targetted metabolism data viewer: export targetted linear modelling report PDF
• enhancement Enable display the RGB ms-imaging renering plot by default when load plot data from the export cdf matrix file comes from the mzkit RGB ms-imging rendering result
• update Add options for group the un-tagged pixel spots in the ms-imging slide sample in the ms-imaging tissue sample region editor
• update Add option for view sample region MS1 spectrum in the ms-imaging tissue sample region editor, use the mouse right click to invoke this function
• update Add option for set custom color in html color code for the ms-imaging tissue sample region
• update Add function for load all annotated molecule layer from the ms-imaging raw data file, you can use this new function via mouse contex menu of the ion layer selector
• update Add batch export of the ms-imaging layer image via mouse contex menu of the ion layer selector
• new Add app plugin for view mzkit LCMS reference spectrum library data pack file, use this function by open plugin from [Plugin Manager] -> [Reference Library Viewer]
• new Add app plugin for access to the Spectrum cluster tree database, use this function by open plugin from [Plugin Manager] -> [Molecular Network Viewer Client]

Ver 4.1.9.5689

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.

Downloads: http://www.biodeep.cn/downloads?lang=en-US

🎉🎇🎇2023
🎉Happy chinese new year!
🧨🧨🧨🎉🎉🎇🎇

• fixed Make bugs fixed for the web query cache system: empty cache could make the empty query result always returned, now it has been fixed!
• new Add mzkit background services process viewer
• new Reconstruct of the mzkit workbench desktop application framework for implements the plugin feature, the mzkit app sotre online
  services is comming soon!
• enhancement fixed for the possible null reference error and the index out of range error, make the MS-imaging viewer more stable
• enhancement make improvements of the task progress UI
• enhancement add copy text and save log output text function to the log text output window
• new Add custom action for view scatter 3d data on the table data.
• new View spatial metabolism tissue spot cluster data in 3d scatter plot view
• new Add new feature for connect to the cloud services for processing ms-imaging data analysis and visualization
• new Add a new feature for view virtual pathology slide in tiff, dzi or ndpi format!
• new View NMR raw data spectrum
• new View 3D MALDI scan data, MS-imaging in 3D
• new Add single cell metabolism data processing feature into the mzkit R# package!
• enhancement Add data context menu in the spectrum matrix viewer: [Open in table view] for send the spectrum matrix to the table viewer for the further data analysis or visualization, and the [Save] menu item for export the selected spectrum matrix into an excel file.
• enhancement Add shortcut button for launch the ms data file conversion tool
• new Merge multiple ms-imaging sample data file into one larger slide, and you also can custom the sample location layout in a super easy way
• new Add an excited feature which you can make the spatial mapping between the spatial transcription sample slide and the spatial metabolism sample slide!
• enhancement make improvements of the ms-imaging render output post image processing function
• fixed make bugs fixed for the in-correct slide scan width and height when do background clean in manually.
• enhancement change the [install Mzkit] button from install package internally to calling the external pipeline script for initialize the R# runtime environment.
• update make improvements of the MS-imaging viewer, update to v2.0 version: do zoom, rotation of the ms-imaging output
• update Add parameter adjustment for the peak finding algorithm page
• enhancement Add functional buttons/context menu to the peak finding page: save matrix, imports matrix and copy peak list data.
• enhancement Add options for check sample row data normalization when do row sample data merge of the MS-imaging row scans.

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Full Changelog: 3.5.593.3968...4.1.9.5689

3.5.593.3968

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.

Downloads: http://www.biodeep.cn/downloads?lang=en-US

• new add tissue morphology map overlaps to MSI viewer
• new add tissue morphology map editor feature to create custom tissue region for data analysis
• new add HE stain image analysis module
• new add a new general table data viewer for open microsoft excel table files
• new add a general data visualization module for plot data based on the table viewer content
• new add new ggplot package for data plot pipeline task
• enhancement add data visualization template rendering for MS-imaging plot
• enhancement enable view multiple sample MS-imaging data
• enhancement add online pubchem metabolite database query function for the ion feature in MSI raw data
• enhancement add data compatibility with the bruker SCiLS lab software
• enhancement make improvements of the ms1 peak list data annotation function
• enhancement update internal metabolite database, extends database list from KEGG only to KEGG/lipidmaps/chebi
• enhancement make the molecular networking viewer interactive
• enhancement add ms1 peak deconvolution function to raw data viewer
• enhancement add peak finding analysis feature to the general signal data analysis
• enhancement new application installer experience
• enhancement upgrade the internal Rstudio environment from .NET4.8 assembly to .NET6.0 assembly
• enhancement add mzwork project file for share the workspace between the device
• enhancement make improvements of the MRM/GCMS targetted data viewer
• fixed add fix patch script to install internal Rstudio environment
• fixed upgrade mzPack format to version 2.0, make improvements of the data compatibility between the single sample data and multiple sample data
• fixed make bugs fixed of the style tweaking for raw data plot viewer
• fixed handling of the data serialization error when raw data file its file path is a windows UNC path

BioNovoGene Mzkit

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), MS-imaging, build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.

UPDATES

• enhancement improvements of the raw data charting plot styles
• new add peak annotation result for MS matrix viewer
• new targetted quantification linear modelling and sample quantify evaluation (required login BioDeep web services)
• enhancement improvements of the GCMS/LC-MSMS targetted file explorer
• enhancement improvements of the GCMS feature ROI explorer
• enhancement improvements of the document page model
• fixed fixed of R# script editor syntax highlight problem
• update update to latest mzkit R# package
• new add 3D plot of LC-MSMS MRM ion TIC overlaps plot
• enhancement add background task progress display on the status bar
• new add demo scripts into the file explorer

BioNovoGene Mzkit

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), MS-imaging, build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.

Raw Data View in mzkit

1. View LC-MS un-targeted data file: mzML, mzXML
2. View GC-MS targeted data file: CDF
3. View LC-MS/MS targeted MRM data: mzML
4. MS-Imaging supported

BioNovoGene Mzkit

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.

Updates

• fix the bugs of UI initialization bugs

BioNovoGene Mzkit

Mzkit is an open source raw data file toolkit for mass spectrometry data analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), build molecule network, formula de-novo search and de-novo annotation.

This open source mass spectrometry data toolkit is developed at the BioDeep R&D laboratory and brought to you by BioNovoGene corporation.