MZKit

5.13.2024.0917

#Sep 17, 2024#

• new search biodeep database online resource for make a specific ion annotation in metabonomics workbench module
• enhancement make improvements of the table viewer: add send to ms-imaging ion list function
• enhancement make improvements of the spatial expression peaktable generator algorithm: make expression data bootstrapping in MSI data service backend(make bootstrapping in frontend UI in old release, this may crashed the entire workbench window if the data payload is too big)
• enhancement make improvements of the metabonomics workbench module: add peaktable pre-processing, data selection, imports annotation, filter annotation function
• enhancement make improvements of the ms-imaging region operation: enable extract region sample data from the loaded tissue region data.
• enhancement enable make config of the adducts when do ms1 peak annotation search
• fixed make bug fixed for rgb overlaps ms-imaging in old release: when the number of selected ions is less than 3 ion, the export script will be crashed, now it has been fixed
• fixed make error fixed for load kegg compound database
• fixed make error fixed of the possible file stream not released when make ms-imaging peakfile exports, this may crashed the data export script background task process.
• fixed fixed of the un-expected raster data filter when do rgb ions overlaps ms-imaging plot exports
• fixed fix of the data reader of the kegg enrichment viewer: data table field name is mis-matched with the reader, this will carashed the entire workbench program in the old release.
• fixed fixed of config default XIC mass tolerance window in the workbench settings page
• fixed fix of the fragment annotation in lc-ms data viewer
• update enable run batch LC-MS rawdata file deconvolution for get a xcms format liked peaktable result, discussion on github: [Does this page is the result of peak picking? xcms_id?Not AccumulateROI? #30](https://github.com/xieguigang/mzkit/issues/30)
• update add new hatmap color palette to the ms-imaging render: ``Seismic`` and ``Icefire``

🎉🎇🎇2024-09-17
🎉Happy Mid-Autumn Festival!
🧨🧨🧨🎉🎉🎇🎇

5.9.3325.159

#Jun 29, 2024#

• new add single cells metabolomics data viewer module(in version 1)
• fixed fix of the tcp networking module in ms-imaging viewer([see details issue #28](https://github.com/xieguigang/mzkit/issues/28))
• fixed fix the login module for the new biodeep online database services

5.2.7336.3219

#Feb 09, 2024#

• 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!
🧨🧨🧨🎉🎉🎇🎇

4.8.199.3374

#Oct 15, 2023#

• new add a new color scaler palette pattern: Typhoon
• new Add median layer imaging for ms-imaging rawdata
• enhancement enable tweaks of the more parameters when export ms-imaging plot file, example as: color map levels, raster filter pipeline, etc
• enhancement Show the feature list of current mouse cursor selected spot in ms-imaging viewer
• enhancement Show the mass spectrum property information of current mouse cursor selected spot in ms-imaging viewer
• fixed fix of the possible program crashed error when view a specific gene expression heatmap from the Spatial Transcriptome data
• fixed fix of the dzi index problem when view the MZKit hds pack in pathological virtual slide viewer(due to the reason of file name is mis-matched with the dzi index name, now this problem has been fixed)
• update add imports of the 10x Visium h5ad rawdata file, you can just set h5ad file source when imports processed 10x Visium rawdata file, or the additional gene symbol, barcode, spot index information is required when imports the space ranger output file.
• update make update the layout algorithm for display the physical ruler in ms-imaging viewer
• update make updates of the Mummichog algorithm, apply the Monte Carlo method for updates the metabolite annotation candidate list in Mummichog
• update make updates of the Moran index calculation for specific ion layer in ms-imaging rawdata processing

4.7.31.9974

#Sep 29, 2023#

• new add a new ribbon menu button for open the pathological virtual slide file, you can access this new feature via menu [File] -> [Toolkit] -> [Open Slide]
• new add new function for do HE stain image overlap with the ms-imaging slide data
• new enable visualize the kegg enrichment result in network graph viewer, use this function just via access the [KEGG enrichment graph] function in the table visualization
• new add file format supports for open the AP-SMALDI udp project file in ms-imaging viewer
• new add LCMS ms1 scatter data viewer
• new add 3d viewer for the LCMS ms1 scatter data
• new add function for adjust the ms-imaging slide its position automatically, used this new function via the [Auto Location] menu button in the ms-imaging viewer
• enhancement add more file format supports for the mzkit pathological virtual slide viewer, it is based on the openslide library for processing the slide file
• enhancement make updates of the pathological virtual slide viewer, you can make a screenshot, export deep zoom image package from the viewer
• enhancement add splash-id for ms spectrum property display
• enhancement add moran index and moran p-value for ms-imaging property viewer
• enhancement You can tweaks of the ms-imaging render pipeline, via the [Tweaks MSI filters] menu button in the ms-imaging viewer.
• fixed make errors fixed for load KEGG compound library when run peak list annotation
• update Some of the menu icon of mzkit has been updates to Windows11 color icons, menu icon comes from the free icon library website: https://icons8.com/icons
• update Make updates of the ms-imaging plot export function, now you can adjust the plot image size, plot content padding and plot dpi for export both single ion ms-imaging plot and rgb overlaps ms-imaging plot
• update updates the demo pathological virtual slide deep zoom image file
• update add intensity quantile plot in the current layer mz histogram viewer

Chinese people, especially the poets, have a special emotion for the moon. The affections they hold may surpass those of any other nations in the world, forming a special moon sentiment. The sight of the moon can affect their emotions, and arouse their hopes and dreams for the future.
Happy Mid-autumn Festival!

4.5.144.3584-patch1

#Jun 26, 2023#

• enhancement add context menu options for view molecular networking cluster spectrum in [molecular network viewer]
• enhancement add black color into the FlexImaging color palette
• fixed make bugs fixed for load ms-imaging data from Thermo Fisher raw file

4.5.139.9689

#Jun 24, 2023#

• 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.
• 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
• 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]
• 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
• 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
• 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
• 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
• fixed fix of the possible bug in the background R# script data backend when create the ms-imaging heatmap matrix
• update removes the biodeep login condition for the targetted metabolism data handler
• 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

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

4.1.9.5689

#Jan 20, 2023#

• 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!
• 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!
• 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 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
• 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
• enhancement make improvements of the ms-imaging render output post image processing function
• enhancement change the [install Mzkit] button from install package internally to calling the external pipeline script for initialize the R# runtime environment.
• 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.
• 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!
• fixed make bugs fixed for the in-correct slide scan width and height when do background clean in manually.
• 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

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

3.6.729.1547

#Nov 21, 2022#

• new SMILES molecule structure designer, power by Ketcher!
• new CFM-ID workflow for run mass spectrum prediction in level2 based on the SMILES/InChI molecule structure string
• new add plot of the phenograph spot cluster information in ms-imaging viewer
• enhancement improvements of the ms-imaging render parameter grid: add options for turn imaging filter and ruler display
• enhancement make improvements of the workbench home page display
• enhancement make improvements of the UI behaviour of the polygon editor for the ms-imaging sample
• fixed make bugs fixed for generates the gray scale color palette
• fixed fix of the possible app crashed problem when drawing an empty polygon in ms-imaging viewer
• update update to latest mzkit R# package

3.5.593.3968

#Sep 01, 2022#

• 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

1.32.7743.6345

#Mar 14, 2021#

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

1.32.7692.29666

#Jan 22, 2021#

• new MS-imaging
• new View MRM/GCMS SIM data files
• enhancement Add plot tweaks function
• enhancement Improvements of the R# scripting editor
• enhancement Update R# interpreter engine

v1.0.0.2-beta

#Nov 15, 2020#

• new Mass spectrum similarity search
• enhancement Improvements of the content project file model
• fixed Bugs fixed of the mzkit_win32 UI

v1.0.0.1-beta

#Oct 15, 2020#

• new View mzML/mzXML raw data files
• new Formula de-novol search
• new Molecular networking
• new Feature search
• new R# scripting for mzkit automation