José Julián Sierra Álvarez
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8741a1ccae
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Merge branch 'main' into dev/PreprocessingInUI
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2026-01-20 19:24:56 +01:00 |
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Pixelguy14
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977b416579
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most stable version of JuliaMSI
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2025-12-10 20:18:39 -06:00 |
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Pixelguy14
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0164e54d77
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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
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2025-12-08 11:25:42 -06:00 |
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Pixelguy14
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b95b8e500c
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finished frontend preprocessing UI connection, small changes to interactivity
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2025-12-01 12:11:49 -06:00 |
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Pixelguy14
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8b1c2d2722
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simplified imzML parsing, finished interactivity for preprocessing in frontend / backend, and processing spectrums is now possible. added n Spectrum plotting
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2025-11-30 18:12:31 -06:00 |
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Pixelguy14
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11c181b3b3
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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.
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2025-11-29 21:47:51 -06:00 |
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Pixelguy14
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bdd9315796
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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
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2025-11-25 12:53:57 -06:00 |
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Pixelguy14
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8fa92dc0e5
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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
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2025-11-17 13:31:37 -06:00 |
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Pixelguy14
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edfbb77f58
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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
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2025-11-09 13:41:29 -06:00 |
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Pixelguy14
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a8c2dfcc91
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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
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2025-11-06 16:43:34 -06:00 |
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Pixelguy14
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3439a8a4dd
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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
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2025-11-04 17:20:05 -06:00 |
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Pixelguy14
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e13b5ef0cc
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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
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2025-10-31 12:05:03 -06:00 |
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Pixelguy14
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39c92ba850
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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
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2025-10-21 11:56:15 -06:00 |
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Pixelguy14
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39fe2bf52c
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UI now has support for mzml to imzml conversion, made small optimizations to the src folder's API to improve performance
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2025-10-16 10:49:16 -06:00 |
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Pixelguy14
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2fd2b90513
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altered imzML parser to be compatible with timsconverter, small improvements on the UI, other small bug fixes done
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2025-10-13 22:05:56 -06:00 |
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Pixelguy14
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f35acd1d0f
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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
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2025-10-09 12:00:00 -06:00 |
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Pixelguy14
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7a0360ef68
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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
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2025-10-06 14:58:37 -06:00 |
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Pixelguy14
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22c8d9637b
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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
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2025-10-02 13:28:15 -06:00 |
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Pixelguy14
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cd1115368f
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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
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2025-09-29 10:57:11 -06:00 |
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Pixelguy14
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b1d7838a60
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Implemented imzml and mzml lazy loading, imzml to load spectra matrix, working on mzml to imzml
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2025-09-25 10:42:33 -06:00 |
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LabABI Cinvestav Irapuato
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3d2deeccfe
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Merge pull request 'Made readme instructions clearer' (#1) from pixxelguy14/JuliaMSI:main into main
Reviewed-on: https://codeberg.org/LabABI/JuliaMSI/pulls/1
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2025-04-10 21:32:56 +00:00 |
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Pixelguy14
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710c74a6c4
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Made readme instructions clearer
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2025-04-10 11:14:04 -06:00 |
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Robert Winkler
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bca4a3c31e
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MIT license added.
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2025-03-20 11:24:01 -06:00 |
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Robert Winkler
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86db0bf03a
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MIT license added.
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2025-03-20 11:20:26 -06:00 |
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Pixelguy14
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074186573c
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Renamed to JuliaMSI
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2025-03-19 09:50:27 -06:00 |
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Pixelguy14
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2bd2e819a4
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Concept error in Sum spectrum, changed to Mean spectrum
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2025-03-13 13:49:49 -06:00 |
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Pixelguy14
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8e1c473acb
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median filter border fix, files get renamed if they don't have correct extension
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2025-03-09 14:02:53 -06:00 |
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Pixelguy14
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421d594b99
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Added test data link in Readme, fixed typo
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2025-03-05 12:29:12 -06:00 |
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Pixelguy14
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3714b404cd
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Fixed scales on plots Topography, Surface and axis on spectrum
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2025-02-20 15:22:54 -06:00 |
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Pixelguy14
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0456abb70b
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Smaller changes to the styling, altered topology layout to use more space
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2025-02-19 21:19:20 -06:00 |
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Pixelguy14
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14af947433
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Minor text corrections, file loading corrections
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2025-02-19 11:32:34 -06:00 |
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Pixelguy14
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e63f9e29e5
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SUM spectrum now loads when loading mzML
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2025-02-15 17:58:39 -06:00 |
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Pixelguy14
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e3e987f0cd
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Fixed some errors to get ready for release
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2025-02-15 15:40:13 -06:00 |
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Pixelguy14
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455d88cbb7
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Included environment variable to set up production, fixed plot errors and optical image load, started mzML to imzML function
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2025-02-13 15:34:13 -06:00 |
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Pixelguy14
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2b6ec4937f
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Fixed bounding error in the median filter application
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2025-02-10 18:41:26 -06:00 |
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Pixelguy14
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63c7428214
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Implemented an experimental executable for all systems, fixed a few errors, implemented first try for a median filter for the slices in Julia
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2025-02-10 15:34:30 -06:00 |
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Pixelguy14
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59630bdd95
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Now the comparative view offers more options to compare to, fixed small mistakes
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2025-02-08 18:36:49 -06:00 |
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Pixelguy14
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47bba11f15
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Small fixes regarding the spectra, topographic and surface plots
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2025-02-06 15:24:29 -06:00 |
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Pixelguy14
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fe6508ead8
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added better margins for image views, implemented upload of optical image and transparency slider
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2025-02-03 22:53:08 -06:00 |
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José Julián Sierra Álvarez
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09d680db87
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Merge pull request #7 from Pixelguy14/Experimental_ColorLevels
Experimental color levels done
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2025-01-30 18:18:53 -06:00 |
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Pixelguy14
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11349330a4
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colorbar scale for both with triq filter and without is finished
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2025-01-30 18:17:32 -06:00 |
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Pixelguy14
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fdd625d3e0
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Bitmap is now normalized in creation, which evenly distributes colors of the colorTable better, now IntQuant allows for coloLevel adjustments
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2025-01-30 00:40:01 -06:00 |
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Pixelguy14
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df0d82910b
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Alternative versions of SaveBitMap and IntQuant for adjustments to the color level input
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2025-01-29 15:55:30 -06:00 |
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Pixelguy14
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4ea5d8e119
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Now the file picker allows for mzML choosing, minor changes to the colorbarplots
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2025-01-28 00:11:19 -06:00 |
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Pixelguy14
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e5e6284d53
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first patch to fix colorbar coherence with R
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2025-01-27 18:10:44 -06:00 |
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Pixelguy14
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7667bc26e9
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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
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2025-01-26 13:48:18 -06:00 |
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Pixelguy14
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b660d7defb
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Minor fixes
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2025-01-23 12:45:48 -06:00 |
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Pixelguy14
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09e4a015e0
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Added plot interaction to the UI, improved boot loading, modified UI to accomodate for these changes
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2025-01-22 23:58:06 -06:00 |
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Pixelguy14
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bf50d0cb0c
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started the inclusion of click interaction for plots
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2025-01-20 16:24:19 -06:00 |
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Pixelguy14
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b913bf5117
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minor fixes regarding colorbarplot
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2025-01-20 15:39:44 -06:00 |
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