DOI: 10.5281/zenodo.14822996
title: Exploring high PT experimental charges through the lens of phase maps: Dataset

description: Main dataset

This dataset contains the files required to reproduce the figures and findings delivered in Kamber et al. (2025) "Exploring high PT experimental charges through the lens of phase maps"

The folders contains:



scripts_update = scripts to generate the phase maps after QuPath segmentation ('qupathPhaseMap_v10_simplified.m') and re-stitch an AMICS software montage.

UHP32_21_40_whole sample_QuPath segmentation = QuPath segmentation phase maps presented in the figures.

UHP32_AMICS Data_auto-stitched = direct AMICS software montage output with different acquisition settings.

UHP32_AMICS Data_re-stitched = image tiles manually exported from AMICS software that need to be processed with the 'imageJ_stack_matthew_v3.py' script.

UHP32_detailed AMICS map_QuPath segmentation benchmark = QuPath segmentation phase map using the output montages from 'UHP32_AMICS Data_re-stitched' folder.

UHP32_TIMA_whole sample_custom library = folder containing the whole sample TIMA phase map after using the custom library.

UHP32_TIMA-AMICS comparison_Figure 9 crop = folder containing the comparison image stacks between the AMICS and TIMA experiments in SEM backscattered electrong (BSE) imaging mode.


The sub-folder structure is (depth 2):

F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitchedF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_auto-stitchedF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom libraryF:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentationF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmarkF:\Zenodo_Kamber et al. 2025\scripts_updateF:\Zenodo_Kamber et al. 2025\UHP32_TIMA-AMICS comparison_Figure 9 cropF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 32F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported framesF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 8F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 16F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 32\BSEF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 32\MineralF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 32\outputF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 32\output2F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\BSEF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\MineralF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\trakem2.1733695048663.26926198.2073909859F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\trakem2.1733695088287.26926198.2073909859F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\trakem2.1733720140791.26926198.2073909859F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\trakem2.1733722222498.26926198.2073909859F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\trakem2.1733723879137.26926198.2073909859F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\trakem2.1733726613532.26926198.2073909859F:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Matrix Mapping exported frames\outputF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 8\BSEF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 8\MineralF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 16\BSEF:\Zenodo_Kamber et al. 2025\UHP32_AMICS Data_re-stitched\Particle Mapping_scan speed 16\MineralF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\UHP32_TIMA_QuPath segmentation_bulkF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\newLibrary_18apr24_MarcoF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\TIMA metadata logF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\UHP32_TIMA_QuPath segmentation_bulk\QUPath_segmentation_projectF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\UHP32_TIMA_QuPath segmentation_bulk\UHP32_tima default exportF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\newLibrary_18apr24_Marco\custom_library_dotMapping_trial1F:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\newLibrary_18apr24_Marco\custom_library_trial1F:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\newLibrary_18apr24_Marco\custom_library_trial2F:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\newLibrary_18apr24_Marco\default_TIMA libraryF:\Zenodo_Kamber et al. 2025\UHP32_TIMA_whole sample_custom library\newLibrary_18apr24_Marco\standardsF:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#21F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#40F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#32F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#21\EDX_21F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#21\HR_BSE_21F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#40\EDX_40F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#40\HR_BSE_40F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#32\High_Resol_panorama_32_2F:\Zenodo_Kamber et al. 2025\UHP32_21_40_whole sample_QuPath segmentation\#32\QUPath_segmentation_projectF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNRF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_TIMAF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\EDX_item 1F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\registration_11-Apr-24F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712280071953.546507025.450761598F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712295256565.546507025.450761598F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712297199695.546507025.450761598F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\coarse_montageF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\fine_montageF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s10F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s3F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s4F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s5F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s6F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s7F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s8F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\#32_MIRA-Image Snaper SNR\s9F:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\EDX_item 1\32#2-DotF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\EDX_item 1\32#2-HRF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\registration_11-Apr-24\registeredF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\registration_11-Apr-24\stacks_tilesF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\registration_11-Apr-24\unregisteredF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712280071953.546507025.450761598\features.serF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712280071953.546507025.450761598\pointmatches.serF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712280071953.546507025.450761598\trakem2.masksF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712280071953.546507025.450761598\trakem2.mipmapsF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712295256565.546507025.450761598\trakem2.mipmapsF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712297199695.546507025.450761598\features.serF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712297199695.546507025.450761598\pointmatches.serF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712297199695.546507025.450761598\trakem2.itsF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712297199695.546507025.450761598\trakem2.masksF:\Zenodo_Kamber et al. 2025\UHP32_detailed AMICS map_QuPath segmentation benchmark\trakem2.1712297199695.546507025.450761598\trakem2.mipmaps

Further information might be requested to the main authors.