Download Report IEEE DataPort : Central Texas Soil Fungi Segmentation 2025
MAT, PNG, JPG, EXR by Alec Graves
Information
Format: MAT, PNG, JPG, EXR Publisher: IEEE DataPort Publication Date of the Electronic Edition: 02/12/2026
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ISBN: 10.21227/wv1a-tr11
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Description
Soil fungi play an important role in many ecosystems: aiding in nutrient cycling, improving plant nutrient uptake, building soil structure and stabilizing soil carbon reserves, and serving as a natural immune system against opportunistic pathogens (through several mechanisms including resource competition). Many plants are not able to grow and survive without soil fungi.This dataset consists of labeled soil smear microscopy images taken from urban natural area (park) sites in south-central Texas within 300 mi of San Antonio, TX, USA. Labels include semantic segmentation masks highlighting fungal hyphae.39 surface soil samples were collected from field sites, placed on ice for transport to the lab, sieved to 1-2mm, and frozen at -20 C. Over a year later (January 2025), samples were mechanically dispersed 1:19 (v/v) into a 0.25g/L aniline blue sodium salt solution through 1hz shaking for 30 seconds, rotated for 3 minutes at 30rpm in a tube rotator, pipette'ed (30ul) onto a glass slide, covered with an 18x18mm cover slip, and imaged through 10x and 40x objectives of a Motic 410E in an oblique light microscopy configuration with an attached biovid 4k camera. Images were captured at random spacing along 5 parallel transects over the slide cover. Fungal hyphae in these micrographs were manually labeled using the Sieve V1 soil fungi labeling tool (https://sr.ht/~alecgraves/sieve/) - the user selects a constant width for each fungal hyphae strand identified. Some site images were extracted from microscope video using ffmpeg ("frame_...").DATASET STRUCTUREEach sample is identified by a site and replicate id. The first number is the site id, and the letter is the replicate id (taken at the same site). For each sample, there are two folders of microscope images, one for the 10x magnification objective and one for the 40x objective. The folders of this dataset are labeled as `<Site ID>-<Replicate ID>_<Objective Magnification>`.Each folder contains randomly spaced images taken along 5 parallel transects over the cover slip, .wxf (Wolfram Exchange Format) label data files, and binary \_mask.png files containing semantic segmentation masks of fungal hyphae drawn from the .wxf label files. The .wxf data files contain the raw user-specified hyphae locations and metadata about whether the user indicated the image was a repeat frame or should be skipped (e.g., due to being blurry or containing a bubble).Example tree output:.├── 1234-A_10x│ ├── IMG_1912.jpg│ ├── IMG_1912_mask.png│ ├── IMG_1912.wxf│ ├── IMG_1913.jpg│ ├── IMG_1913_mask.png│ ├── IMG_1913.wxf| ├──...├── 1234-A_40x│ ├── frame_001.jpg│ ├── frame_001.wxf│ ├── frame_002.jpg│ ├── frame_003.wxf│ ├── frame_003.jpg│ ├── frame_003_mask.pngImportant notes:Mask image files are only created for positive images containing fungal hyphae.Only the 'A'-labeled 10x replicates are guaranteed to have 10x labels since 10x labels take longer to create due to the larger field of view to analyze. All 40x sites and replicates were labeled.The 'calibration' folder contains stage-micrometer calibration target images for the Motic 410e microscope 4x, 10x, and 40x objectives (1 tick = 10 micrometer).DATA AVAILABILITY STATEMENTThis dataset was developed with support from the USDA Natural Resources Conservation Service "Addressing the Soil-Microbial Gap", award no. NR233A750023C049.In accordance with U.S. Department of Agriculture (USDA) Departmental Regulation 1020-006 Section 5a, "It is USDA policy to provide public access to all scholarly publications and digital scientific research data assets that arise from USDA-supported scientific research." Section 5c(4) requires that "digital scientific research data assets covered by public access requirements should be made publicly accessible as soon as possible, and within 12 months of the publication date of an associated scholarly publication, or the end of the performance or funding period, whichever comes first."This dataset is made publicly available in compliance with these federal requirements and is released under the Creative Commons Attribution 4.0 International License (CC-BY 4.0).Associated publication: https://doi.org/10.7185/gold2025.26258Any opinions, findings, conclusions, or recommendations expressed in this dataset are those of the author(s) and do not necessarily reflect the views of the U.S. Department of Agriculture.Copyright (C) 2026 Alec Graves
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