Julian/JuliaMSI
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  • 2198845aae Merge pull request 'dev/Memory_pooling_adjustments' (#1) from dev/Memory_pooling_adjustments into main main José Julián Sierra Álvarez 2026-05-31 01:03:57 +02:00
  • 89de5a56e0 Fixed small issues within the file load and the precompiler script, added a final test benchmark suit to compare old Julia MSI library with current dev/Memory_pooling_adjustments Pixelguy14 2026-04-16 16:39:31 -06:00
  • 05cb79253f cleaned the repository from dead code, simplified some functions, users can now create a system image of the JuliaMSI repo that runs the core dependencies faster without compiler time, alongside a docker environment for running scripts, the instructions are on the readme Pixelguy14 2026-04-09 13:46:30 -06:00
  • 8c37ea64aa fixed disk and memory bloat when loading several files, created zero-copy mmaps for msidata type objects for easier cache storage and less memory overhead, improved load times for files in general across the whole JuliaMSI environment Pixelguy14 2026-04-09 12:30:43 -06:00
  • 70fff16170 more secure locks and a script to create a system image of juliaMSI for faster boot times, still experimental but everything else remains pristine dev/Adjustments Pixelguy14 2026-04-07 14:06:02 -06:00
  • e0ef601a9b hopefully fixed the JSON Lock for Windows Pixelguy14 2026-04-06 15:41:38 -06:00
  • 8b6bed0ff5 Hot fix to the precalculation atomic variable accountability, and other base threads safety hotfix/bugfixes_12_03 Pixelguy14 2026-03-12 12:51:16 -06:00
  • 3da0dcaae9 Improved documentation, added precautions to te json generation and loading specially for windows Pixelguy14 2026-03-03 14:36:39 -06:00
  • df94d50954 Implemented more multithreaded precautions in precalculations and preprocessing pipeline, added concurrency tests and validations on several datacentric functions, refractored preprocessing pipeline, added visual upgrades to the UI and a clear session and bug report buttons Pixelguy14 2026-02-13 13:42:41 -06:00
  • 4414671a30 Merge pull request 'dev/PreprocessingInUI' (#1) from dev/PreprocessingInUI into main José Julián Sierra Álvarez 2026-01-20 19:26:54 +01:00
  • 8741a1ccae Merge branch 'main' into dev/PreprocessingInUI dev/PreprocessingInUI José Julián Sierra Álvarez 2026-01-20 19:24:56 +01:00
  • 977b416579 most stable version of JuliaMSI Pixelguy14 2025-12-10 20:18:39 -06:00
  • 0164e54d77 Fixed issues in the UI, added benchmark to compare with old juliaMSI library with the new custom one, incorporating platform detection and memory for amplifying cache pools Pixelguy14 2025-12-08 11:25:42 -06:00
  • b95b8e500c finished frontend preprocessing UI connection, small changes to interactivity Pixelguy14 2025-12-01 12:11:49 -06:00
  • 8b1c2d2722 simplified imzML parsing, finished interactivity for preprocessing in frontend / backend, and processing spectrums is now possible. added n Spectrum plotting Pixelguy14 2025-11-30 18:12:31 -06:00
  • 11c181b3b3 Interface ready for preprocessing steps handling. style altered to support modular preprocessing pipeline, finished precalculations and preprocessing code, and its respective testing script, added preprocessingpipeline, a handler for the low level functions of preprocessing to work with the high level MSIData in the genie environment. Pixelguy14 2025-11-29 21:47:51 -06:00
  • bdd9315796 Fixed preprocessing module, implemented precalculations, this code gives a prediction of the values for the parameters in every step for preprocessing, added test suites for both the parameter generation and the preprocessing pipeline, included a descriptive processing that returns an image with what every parameter does in every step, added instrument metadata structure with the parser for each type of file, to retrieve several important parameters to automate precalculations and preprocessing dev/ProcessingWithMasks Pixelguy14 2025-11-25 12:53:57 -06:00
  • 8fa92dc0e5 improved preprocessing UI, added selective spectrum plot accordig to type (centroid, profile), potentially fixed a bug to retrieve folders on dropdown selectors in startup, improved preprocessing functions and test suite, testing a version control for preprocessing steps Pixelguy14 2025-11-17 13:31:37 -06:00
  • edfbb77f58 Added bloom filters custom API, thread safety for multithreading several important functions, streaming processing to reduce GC and Memory allocations calls, buffer pool changed with lock safety, and debug memory monitoring to track leaks, alongside better loading times in general Pixelguy14 2025-11-09 13:41:29 -06:00
  • a8c2dfcc91 Implementing foundations for multithreading, standarized mzml converter, profile/centroid detection per pixel, memory-efficient buffer reuse, added preparations to bloom filter alongside buffer pulling, removed memory leaks on linux due to @async macro used on @app module, better error management Pixelguy14 2025-11-06 16:43:34 -06:00
  • 3439a8a4dd Added mask interface accessible from the UI, with it you can create slices from your masks or your images of the samples, included masking in the main processing, on the spectra creation, and on the 3d surface plot, started with interface for pre processing spectral data Pixelguy14 2025-11-04 17:20:05 -06:00
  • e13b5ef0cc finished mask creator suite, a new route on the JuliaMSI which helps to create binary masks using either slices or added images, with drawing capability, which in turn will help in the future get more accurate results without extra ambiental noise, added preprocessing test pipeline, along with functions, fixed windows route error for batch processing dev/AdvancedProcessingAPI Pixelguy14 2025-10-31 12:05:03 -06:00
  • 39c92ba850 bulk and batch processing for multiple imzml and multiple m/z is now available, folder organization for imzml slices in public folder, JSON tracking of processed datasets to save memory time, multiple performance optimizations and UI bug fixes, metadata viewing for all processed files, comparative view between multiple datasets Pixelguy14 2025-10-21 11:56:15 -06:00
  • 39fe2bf52c UI now has support for mzml to imzml conversion, made small optimizations to the src folder's API to improve performance Pixelguy14 2025-10-16 10:49:16 -06:00
  • 2fd2b90513 altered imzML parser to be compatible with timsconverter, small improvements on the UI, other small bug fixes done Pixelguy14 2025-10-13 22:05:56 -06:00
  • f35acd1d0f updated functions to iterate faster to create imzml images (find_mass, get_mz_slice, _iterate_spectra_fast, get_total_spectrum) metadata adquisition and saving, updated docstrings, started work for parser to detect 4 cases, profile uncompressed (current), profile compressed, centroid uncompressed, centroid compressed dev/FasterXMLDataAccess Pixelguy14 2025-10-09 12:00:00 -06:00
  • 7a0360ef68 added docstrings to most functions in the src folder, altered msi data calculations for fast iterators, improved total spectrumtimes, added closer colorbar bin calculations, plus more small changes Pixelguy14 2025-10-06 14:58:37 -06:00
  • 22c8d9637b integrated MSI_src API into the UI, fixed interface elements, made some processes asynchronous, modified spectrum plots, added sum spectrum, removed use of obsolete julia_mzML_imzML library Pixelguy14 2025-10-02 13:28:15 -06:00
  • cd1115368f finished test script, included instructions in test/readme.md, the test performs mzml, imzml and conversion tests, along with throwing reference plots and images which result from the files Pixelguy14 2025-09-29 10:57:11 -06:00
  • b1d7838a60 Implemented imzml and mzml lazy loading, imzml to load spectra matrix, working on mzml to imzml Pixelguy14 2025-09-25 10:42:33 -06:00
  • 3d2deeccfe Merge pull request 'Made readme instructions clearer' (#1) from pixxelguy14/JuliaMSI:main into main LabABI Cinvestav Irapuato 2025-04-10 21:32:56 +00:00
  • 710c74a6c4 Made readme instructions clearer Pixelguy14 2025-04-10 11:14:04 -06:00
  • bca4a3c31e MIT license added. Robert Winkler 2025-03-20 11:24:01 -06:00
  • 86db0bf03a MIT license added. Robert Winkler 2025-03-20 11:20:26 -06:00
  • 074186573c Renamed to JuliaMSI Pixelguy14 2025-03-19 09:50:27 -06:00
  • 2bd2e819a4 Concept error in Sum spectrum, changed to Mean spectrum Pixelguy14 2025-03-13 13:49:49 -06:00
  • 8e1c473acb median filter border fix, files get renamed if they don't have correct extension Pixelguy14 2025-03-09 14:02:53 -06:00
  • 421d594b99 Added test data link in Readme, fixed typo Pixelguy14 2025-03-05 12:29:12 -06:00
  • 3714b404cd Fixed scales on plots Topography, Surface and axis on spectrum Pixelguy14 2025-02-20 15:22:54 -06:00
  • 0456abb70b Smaller changes to the styling, altered topology layout to use more space Pixelguy14 2025-02-19 21:19:20 -06:00
  • 14af947433 Minor text corrections, file loading corrections Pixelguy14 2025-02-19 11:32:34 -06:00
  • e63f9e29e5 SUM spectrum now loads when loading mzML Pixelguy14 2025-02-15 17:58:39 -06:00
  • e3e987f0cd Fixed some errors to get ready for release Pixelguy14 2025-02-15 15:40:13 -06:00
  • 455d88cbb7 Included environment variable to set up production, fixed plot errors and optical image load, started mzML to imzML function Pixelguy14 2025-02-13 15:34:13 -06:00
  • 2b6ec4937f Fixed bounding error in the median filter application Pixelguy14 2025-02-10 18:41:26 -06:00
  • 63c7428214 Implemented an experimental executable for all systems, fixed a few errors, implemented first try for a median filter for the slices in Julia Pixelguy14 2025-02-10 15:34:30 -06:00
  • 59630bdd95 Now the comparative view offers more options to compare to, fixed small mistakes Pixelguy14 2025-02-08 18:36:49 -06:00
  • 47bba11f15 Small fixes regarding the spectra, topographic and surface plots Pixelguy14 2025-02-06 15:24:29 -06:00
  • fe6508ead8 added better margins for image views, implemented upload of optical image and transparency slider Pixelguy14 2025-02-03 22:53:08 -06:00
  • 09d680db87
         Merge pull request #7 from Pixelguy14/Experimental_ColorLevels José Julián Sierra Álvarez 2025-01-30 18:18:53 -06:00
  • 11349330a4 colorbar scale for both with triq filter and without is finished Pixelguy14 2025-01-30 18:17:32 -06:00
  • fdd625d3e0 Bitmap is now normalized in creation, which evenly distributes colors of the colorTable better, now IntQuant allows for coloLevel adjustments Pixelguy14 2025-01-30 00:40:01 -06:00
  • df0d82910b Alternative versions of SaveBitMap and IntQuant for adjustments to the color level input Pixelguy14 2025-01-29 15:55:30 -06:00
  • 4ea5d8e119 Now the file picker allows for mzML choosing, minor changes to the colorbarplots Pixelguy14 2025-01-28 00:11:19 -06:00
  • e5e6284d53 first patch to fix colorbar coherence with R Pixelguy14 2025-01-27 18:10:44 -06:00
  • 7667bc26e9 Images are now plots, now you can select the pixel of the plot to create a spectra according to those coordenates, gave more clearness to the code by creating functions for some processes Pixelguy14 2025-01-26 13:48:18 -06:00
  • b660d7defb Minor fixes Pixelguy14 2025-01-23 12:45:48 -06:00
  • 09e4a015e0 Added plot interaction to the UI, improved boot loading, modified UI to accomodate for these changes Pixelguy14 2025-01-22 23:58:06 -06:00
  • bf50d0cb0c started the inclusion of click interaction for plots Pixelguy14 2025-01-20 16:24:19 -06:00
  • b913bf5117 minor fixes regarding colorbarplot Pixelguy14 2025-01-20 15:39:44 -06:00
  • d18b113641 added time measurements for main functions of the app Pixelguy14 2025-01-19 17:07:04 -06:00
  • c92576d5a5 Finished tabs and compare views, added file search to ease access to files, corrected minimal fixes Pixelguy14 2025-01-16 16:22:32 -06:00
  • ddc690b659 make buttons disabled when other process is running, added tabs, added comparative view, added rotation to taller images Pixelguy14 2025-01-15 21:15:02 -06:00
  • 13a5f7f222 3d plot fixes and UI corrections Pixelguy14 2025-01-15 15:45:03 -06:00
  • e3cd15157e fixed genie package install Pixelguy14 2025-01-15 11:38:49 -06:00
  • 645d569f03 Finished the 3d plot topology for images, added contour plots for images, added algebra, fixed image vertical flipping, experimental changes for a faster first boot Pixelguy14 2025-01-14 20:57:42 -06:00
  • c2ffbc8275 3d plot contours, fixed startup script Pixelguy14 2025-01-13 12:50:57 -06:00
  • e5b796fce0 Better image search, 3d images ongoing Pixelguy14 2025-01-13 00:56:12 -06:00
  • 04f7a107da Quicker start for the app, better UI, More responsiveness, code cleaning, and more readability for the code Pixelguy14 2025-01-11 22:14:24 -06:00
  • d30b5d173b Set maximum height to images to avoid extension of page size Pixelguy14 2024-11-06 14:13:54 -06:00
  • 1dd7eed839
         Merge pull request #6 from Pixelguy14/test/multiplataform José Julián Sierra Álvarez 2024-10-18 10:32:26 -06:00
  • c0418c4ff0
         Update README.md ING-HGA 2024-10-17 16:53:04 -06:00
  • 72cb64e731
         Testing condition to avoid errors in macOS José Julián Sierra Álvarez 2024-10-12 11:18:22 -06:00
  • faca7c82cb
         Update README.md ING-HGA 2024-10-07 16:13:48 -06:00
  • 309babecee
         Update README.md ING-HGA 2024-10-03 10:34:12 -06:00
  • d7371ee34a
         Update README.md ING-HGA 2024-10-03 10:31:58 -06:00
  • b8faab7a89
         Update README.md José Julián Sierra Álvarez 2024-09-30 12:27:37 -06:00
  • ae7b1380fe
         Style update José Julián Sierra Álvarez 2024-09-22 19:46:31 -06:00
  • ad97065360
         Corrected an issue related to the colorbar plot José Julián Sierra Álvarez 2024-09-19 20:59:32 -06:00
  • f251b8cebc
         Update .gitignore José Julián Sierra Álvarez 2024-09-18 21:18:12 -06:00
  • 7773b5d566
         added LABI logo José Julián Sierra Álvarez 2024-09-18 21:16:21 -06:00
  • 1caf0a76c3
         Added Colorbar for each slice of scan José Julián Sierra Álvarez 2024-09-18 21:15:18 -06:00
  • 2aaa53ee42
         Optimized memory cleaning, Improved UX/UI design José Julián Sierra Álvarez 2024-09-13 17:11:32 -06:00
  • 026b43daee
         Revision of plot view José Julián Sierra Álvarez 2024-09-11 19:24:16 -06:00
  • f08366bc12
         Delete public/TrIQ_170.bmp José Julián Sierra Álvarez 2024-09-11 19:04:50 -06:00
  • f1404f48e6
         Delete public/TrIQ_100.bmp José Julián Sierra Álvarez 2024-09-11 19:04:38 -06:00
  • d955c9f0a0
         Add files via upload José Julián Sierra Álvarez 2024-09-11 16:23:09 -06:00
  • e7e751c143
         Improved the way it handles plotting José Julián Sierra Álvarez 2024-09-11 15:55:00 -06:00
  • 60441a28d8
         Added Statistics for mean plot values José Julián Sierra Álvarez 2024-09-11 12:35:15 -06:00
  • e5824dd858
         Fixed the functionality of plot for the imzML file José Julián Sierra Álvarez 2024-09-11 11:32:06 -06:00
  • 642d2044cd
         Update README.md José Julián Sierra Álvarez 2024-09-11 09:49:10 -06:00
  • 3bef29a8a9
         Merge pull request #5 from Pixelguy14/dev/bazzite José Julián Sierra Álvarez 2024-08-21 14:46:37 -06:00
  • 28336b6624
         Merge branch 'main' into dev/bazzite José Julián Sierra Álvarez 2024-08-21 14:46:01 -06:00
  • cd56bd5e4a added plots, resolved some issues Pixelguy14 2024-08-21 14:44:13 -06:00
  • 3811c7e331
         Update README.md José Julián Sierra Álvarez 2024-08-21 11:52:28 -06:00
  • ca9f5f3770
         Merge pull request #4 from Pixelguy14/dev/bazzite José Julián Sierra Álvarez 2024-08-21 11:47:45 -06:00
  • 3fd628f5cf Updated routes for files and cleaned the interface Pixelguy14 2024-08-21 11:45:50 -06:00
  • 0ea5485f28
         Add files via upload Pixelguy14 2024-07-31 19:35:15 -06:00
  • 3650572337
         Add files via upload Pixelguy14 2024-07-31 19:34:54 -06:00
  • 11b0dc493c
         Update README.md Pixelguy14 2024-07-31 19:20:00 -06:00