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Recent Releases of mzkit

mzkit - 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 https://github.com/xieguigang/mzkit/pull/24
  • Oligonucleotide ms by @xieguigang in https://github.com/xieguigang/mzkit/pull/25
  • Update README.md by @xieguigang in https://github.com/xieguigang/mzkit/pull/26

Full Changelog: https://github.com/xieguigang/mzkit/compare/4.5.139.9689...5.2.7336.3219

Capture

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

- Visual Basic .NET
Published by xieguigang almost 2 years ago

mzkit - 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

screenshot

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]

- Visual Basic .NET
Published by xieguigang over 2 years ago

mzkit - 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

Capture

🎉🎇🎇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.

Full Changelog: https://github.com/xieguigang/mzkit/compare/3.5.593.3968...4.1.9.5689

- Visual Basic .NET
Published by xieguigang almost 3 years ago

mzkit - 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

- Visual Basic .NET
Published by xieguigang over 3 years ago

mzkit - 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

Targeted

- Visual Basic .NET
Published by xieguigang almost 5 years ago

mzkit - 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

ms-imaging1

- Visual Basic .NET
Published by xieguigang almost 5 years ago

mzkit - 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

- Visual Basic .NET
Published by xieguigang about 5 years ago

mzkit - 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.

MS

- Visual Basic .NET
Published by xieguigang about 5 years ago