cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57907/mirri/4dx2ej/dpmusd
title: MIRRI0122883.json

description: Strain json file
DOI: 10.57907/mirri/aeszc7/qobpq4
title: MIRRI0120965.json

description: Strain json file
DOI: 10.57907/mirri/brzjan/5kjcqz
title: MIRRI0121896.json

description: Strain json file
DOI: 10.57907/mirri/d4lead
title: MIRRI0120969

description: Organism type: Filamentous Fungi ; Taxon name: Nectria vilior ; Collection: MUCL 21952
DOI: 10.57907/mirri/eryz3n/6zreqo
title: MIRRI0122898.json

description: Strain json file
DOI: 10.57907/mirri/esd4hg
title: MIRRI0121599

description: Organism type: Yeast ; Taxon name: Leucosporidium scottii ; Collection: MUCL 28629
DOI: 10.57907/mirri/fejovi/ocbjj3
title: MIRRI0121784.json

description: Strain json file
DOI: 10.57907/mirri/iaus6x/xkeb1t
title: MIRRI0119330.json

description: Strain json file
DOI: 10.57907/mirri/iucroq/nosyk1
title: MIRRI0122931.json

description: Strain json file
DOI: 10.57907/mirri/iwcuwi
title: MIRRI0121549

description: Organism type: Filamentous Fungi ; Taxon name: Brucella daejeonensis ; Collection: MUCL 28496
DOI: 10.57907/mirri/iwcuwi/fqzal7
title: MIRRI0121549.json

description: Strain json file
DOI: 10.57907/mirri/j9jthi/idgloq
title: MIRRI0120906.json

description: Strain json file
DOI: 10.57907/mirri/nhs2pf
title: MIRRI0122899

description: Organism type: Yeast ; Taxon name: Rhodotorula babjevae ; Collection: MUCL 30602 ; Country: Germany
DOI: 10.57907/mirri/nuwtk8
title: MIRRI0121522

description: Organism type: Filamentous Fungi ; Taxon name: Rhizopus oryzae ; Collection: MUCL 28425 ; Country: Canada
DOI: 10.57907/mirri/nyc75m/fw6b6k
title: MIRRI0121553.json

description: Strain json file
DOI: 10.57907/mirri/pflvyw
title: MIRRI0120968

description: Organism type: Filamentous Fungi ; Taxon name: Acremonium chrysogenum ; Collection: MUCL 21947 ; Country: India
DOI: 10.57907/mirri/qj6rdi
title: MIRRI0121528

description: Organism type: Filamentous Fungi ; Taxon name: Hypocrea nigricans ; Collection: MUCL 28439 ; Country: Japan
DOI: 10.57907/mirri/s8tbts
title: MIRRI0121793

description: Organism type: Filamentous Fungi ; Taxon name: Periconia cookei ; Collection: MUCL 28907 ; Country: Burundi
DOI: 10.57907/mirri/sjrf6f/0monta
title: MIRRI0119375.json

description: Strain json file
DOI: 10.57907/mirri/t2dvfk/lbghof
title: MIRRI0120905.json

description: Strain json file
DOI: 10.57907/mirri/v6kgsx
title: MIRRI0120891

description: Organism type: Filamentous Fungi ; Taxon name: Botryotinia porri ; Collection: MUCL 21540 ; Country: United Kingdom
DOI: 10.57907/mirri/vl5ydp
title: MIRRI0121554

description: Organism type: Filamentous Fungi ; Taxon name: Agrocybe praecox ; Collection: MUCL 28505 ; Country: Belgium
DOI: 10.57907/mirri/vp5zgf
title: MIRRI0119388

description: Organism type: Filamentous Fungi ; Taxon name: Humicola nigrescens ; Collection: MUCL 14437 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/xd1a3b
title: MIRRI0122924

description: Organism type: Yeast ; Taxon name: Rhodotorula mucilaginosa var. mucilaginosa ; Collection: MUCL 30630 ; Country: Italy
DOI: 10.57907/mirri/ypdegv/njju4x
title: MIRRI0120887.json

description: Strain json file
DOI: 10.57907/mirri/z8mdd9/7nvqmn
title: MIRRI0121576.json

description: Strain json file
DOI: 10.60875/vfnq-ya17
title: Science Museum Group 1921 Textile Machinery Catalogue

description: The catalogue entries from the Science Museum’s 1921 Textile Machinery catalogue delivered by Felix to Tim under the name ‘Textile_Machinery_Ids_KeyBERT_Annotated_and_NER_v2’ with: regular expressions parsing of catalogue entry titles to create candidate object names; SPD candidate object names, KeyBERT ditto and NER candidate terms. Tim has modified in various ways, including notably researching and entering of inventory numbers for all the objects in the catalogue, the majority of which were listed under archaic ‘M-numbers’; also OpenRefine conversion from uc to lc and various bits of tidying up.
DOI: 10.3535/31y-6eb-4wz
title: Fallopia Adans.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/2qejmw
title: MIRRI0119338

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium vinaceum ; Collection: MUCL 14368 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/hglqtv/anryls
title: MIRRI0119332.json

description: Strain json file
DOI: 10.57907/mirri/qv91xy/rzpb5f
title: MIRRI0121605.json

description: Strain json file
DOI: 10.57907/mirri/xmnwng/cyh2hn
title: MIRRI0119349.json

description: Strain json file
DOI: 10.3535/0ph-x1f-d47
title: Verbascum orientale (L.) All.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/v15-g4b-502
title: Clinopodium graveolens (M.Bieb.) Kuntze

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.15468/dl.srn9kv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Balitora annamitica)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067781-250717081556266/datasets/export for details.
DOI: 10.3535/ptp-wq9-0zj
title: Stipa arabica Trin. & Rupr.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/rd8-7dq-vp2
title: Cystopteris fragilis (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.5281/zenodo.16387131
title: MAPL orchestrates gasdermin-mediated release of mtDNA from lysosomes that drives pyroptotic cell death

description: Cell death is inhibited in cancers but increased in neurodegeneration, highlighting the importance of its regulation for human health. MAPL is an outer mitochondrial membrane SUMO ligase involved in cell death in both cancer and neurodegeneration in vivo, yet how MAPL controls the fate of this process remains unclear. Combining genome-wide functional genetic screening and cell biological approaches, we found that MAPL induces pyroptosis through an inflammatory pathway involving mitochondria and lysosomes. MAPL overexpression promotes mitochondrial DNA (mtDNA) trafficking in mitochondrial-derived vesicles (MDVs) to lysosomes, which are permeabilized in a process requiring gasdermin pores. This triggers the release of mtDNA into the cytosol, activating the DNA sensor cGAS, required for cell death. Additionally, multiple Parkinson’s disease-related genes, including VPS35 and LRRK2, also regulate MAPL-induced pyroptosis. Importantly, depletion of MAPL, LRRK2 or VPS35 inhibited inflammatory cell death in primary macrophages, placing MAPL and the mitochondria-to-lysosome pathway at the nexus of immune signalling and cell death.
DOI: 10.57907/mirri/0awb1f
title: MIRRI0121563

description: Organism type: Filamentous Fungi ; Taxon name: Agaricus hortensis ; Collection: MUCL 28515 ; Country: Belgium
DOI: 10.57907/mirri/0hjidx
title: MIRRI0121649

description: Organism type: Filamentous Fungi ; Taxon name: Pleurotus sajor-caju ; Collection: MUCL 28685 ; Country: Malaysia
DOI: 10.57907/mirri/0vfhhm
title: MIRRI0122953

description: Organism type: Yeast ; Taxon name: Dioszegia hungarica ; Collection: MUCL 30660 ; Country: Hungary
DOI: 10.57907/mirri/16weil
title: MIRRI0123044

description: Organism type: Filamentous Fungi ; Taxon name: Punctularia atropurpurascens ; Collection: MUCL 30786 ; Country: Canada
DOI: 10.57907/mirri/1rebu2
title: MIRRI0119361

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium jensenii ; Collection: MUCL 14394 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/1ssirr
title: MIRRI0121611

description: Organism type: Yeast ; Taxon name: Kluyveromyces marxianus ; Collection: MUCL 28641 ; Country: United Kingdom
DOI: 10.57907/mirri/2ecbs0
title: MIRRI0122954

description: Organism type: Yeast ; Taxon name: Cryptococcus aquaticus ; Collection: MUCL 30661 ; Country: United Kingdom
DOI: 10.57907/mirri/2jdxxl/ajgk6g
title: MIRRI0121830.json

description: Strain json file
DOI: 10.57907/mirri/6avu3f/igepmx
title: MIRRI0120956.json

description: Strain json file
DOI: 10.57907/mirri/8gonpv/p3gm6z
title: MIRRI0122977.json

description: Strain json file
DOI: 10.57907/mirri/8xqsvp
title: MIRRI0121666

description: Organism type: Yeast ; Taxon name: Saccharomyces pastorianus var. pastorianus ; Collection: MUCL 28711 ; Country: China
DOI: 10.57907/mirri/anbkzw/1k6kj1
title: MIRRI0122961.json

description: Strain json file
DOI: 10.57907/mirri/bgtjn3
title: MIRRI0120912

description: Organism type: Filamentous Fungi ; Taxon name: Stachybotrys chartarum ; Collection: MUCL 21685 ; Country: Belgium
DOI: 10.57907/mirri/bhflpn/xxxsgy
title: MIRRI0119335.json

description: Strain json file
DOI: 10.57907/mirri/c2fyhf/rzxspd
title: MIRRI0121631.json

description: Strain json file
DOI: 10.57907/mirri/c92ljm/ejuqjn
title: MIRRI0122964.json

description: Strain json file
DOI: 10.57907/mirri/diosmk
title: MIRRI0122919

description: Organism type: Yeast ; Taxon name: Rhodotorula crocea ; Collection: MUCL 30625 ; Country: South Africa
DOI: 10.57907/mirri/ds6u8m
title: MIRRI0119386

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium simplicissimum ; Collection: MUCL 14435 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/e56qlh
title: MIRRI0121648

description: Organism type: Filamentous Fungi ; Taxon name: Pleurotus citrinopileatus ; Collection: MUCL 28684 ; Country: Malaysia
DOI: 10.57907/mirri/g5ukcf/mbnjco
title: MIRRI0119381.json

description: Strain json file
DOI: 10.57907/mirri/h13pps/mh0a4v
title: MIRRI0122975.json

description: Strain json file
DOI: 10.57907/mirri/hbm7hu/ix1mt5
title: MIRRI0121592.json

description: Strain json file
DOI: 10.57907/mirri/hiqm1m/i8jeb6
title: MIRRI0121587.json

description: Strain json file
DOI: 10.57907/mirri/i7zo9p/fjpoyq
title: MIRRI0122958.json

description: Strain json file
DOI: 10.57907/mirri/ikrjtc
title: MIRRI0121558

description: Organism type: Filamentous Fungi ; Taxon name: Lentinula edodes ; Collection: MUCL 28509 ; Country: Belgium
DOI: 10.57907/mirri/jqph55/e0tuzr
title: MIRRI0122925.json

description: Strain json file
DOI: 10.57907/mirri/lfzywt
title: MIRRI0120927

description: Organism type: Filamentous Fungi ; Taxon name: Nectria vilior ; Collection: MUCL 21746 ; Country: Belgium
DOI: 10.57907/mirri/m2lovj
title: MIRRI0119334

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium simplicissimum ; Collection: MUCL 14364 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/mgyffv/cg27zd
title: MIRRI0120995.json

description: Strain json file
DOI: 10.57907/mirri/n56beu
title: MIRRI0122986

description: Organism type: Filamentous Fungi ; Taxon name: Heterobasidion annosum ; Collection: MUCL 30709 ; Country: Belgium
DOI: 10.57907/mirri/nfgvsc
title: MIRRI0120928

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus tubingensis ; Collection: MUCL 21747 ; Country: Morocco
DOI: 10.57907/mirri/ouqwgb
title: MIRRI0122911

description: Organism type: Yeast ; Taxon name: Vanrija humicola ; Collection: MUCL 30614
DOI: 10.57907/mirri/pakktp/auv5p3
title: MIRRI0122901.json

description: Strain json file
DOI: 10.57907/mirri/pue9yx/gy5zj1
title: MIRRI0122920.json

description: Strain json file
DOI: 10.57907/mirri/tfykm2/h63o57
title: MIRRI0120950.json

description: Strain json file
DOI: 10.57907/mirri/tlcycz
title: MIRRI0122968

description: Organism type: Yeast ; Taxon name: Sporidiobolus ruineniae var. ruineniae ; Collection: MUCL 30685 ; Country: Japan
DOI: 10.57907/mirri/tlcycz/hvnaly
title: MIRRI0122968.json

description: Strain json file
DOI: 10.57907/mirri/todnwe
title: MIRRI0120933

description: Organism type: Filamentous Fungi ; Taxon name: Helicoön richonis ; Collection: MUCL 21788 ; Country: Netherlands
DOI: 10.57907/mirri/tv4ztp
title: MIRRI0120920

description: Organism type: Filamentous Fungi ; Taxon name: Ceratocystis paradoxa ; Collection: MUCL 2170 ; Country: Malaysia
DOI: 10.57907/mirri/ubceab
title: MIRRI0122946

description: Organism type: Yeast ; Taxon name: Cryptococcus curvatus ; Collection: MUCL 30653 ; Country: Germany
DOI: 10.57907/mirri/vmdf1j/8xm4wh
title: MIRRI0121835.json

description: Strain json file
DOI: 10.57907/mirri/wulmyr/absaqx
title: MIRRI0121580.json

description: Strain json file
DOI: 10.57907/mirri/x6fqmq
title: MIRRI0122915

description: Organism type: Yeast ; Taxon name: Papiliotrema laurentii ; Collection: MUCL 30619 ; Country: United States of America
DOI: 10.57907/mirri/ywb3io
title: MIRRI0122909

description: Organism type: Yeast ; Taxon name: Rhodosporidium diobovatum ; Collection: MUCL 30612 ; Country: United States of America
DOI: 10.57907/mirri/ywb3io/ivbpnh
title: MIRRI0122909.json

description: Strain json file
DOI: 10.3535/c04-h3f-qyd
title: Lathyrus cicera L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/nze-ew8-rf5
title: Minuartia meyeri (Boiss.) Bornm.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/ech-fvk-8aj
title: Vicia sativa subsp. nigra Ehrh.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/q07-fpv-mg6
title: Nonea versicolor (Steven) Sweet

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/0kln1v
title: MIRRI0121634

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium dierckxii ; Collection: MUCL 28665
DOI: 10.57907/mirri/byxtee/jrjntf
title: MIRRI0121903.json

description: Strain json file
DOI: 10.57907/mirri/c2fyhf
title: MIRRI0121631

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium commune ; Collection: MUCL 28661 ; Country: Belgium
DOI: 10.57907/mirri/c6dbbk/n09umu
title: MIRRI0121977.json

description: Strain json file
DOI: 10.57907/mirri/duwqdp
title: MIRRI0121932

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium glabrum ; Collection: MUCL 29119
DOI: 10.57907/mirri/es4zig/tejbnv
title: MIRRI0121659.json

description: Strain json file
DOI: 10.57907/mirri/ezlnax/rlv61s
title: MIRRI0121817.json

description: Strain json file
DOI: 10.57907/mirri/gnwbck
title: MIRRI0121973

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium aurantiogriseum var. viridicatum ; Collection: MUCL 29185 ; Country: United Kingdom
DOI: 10.57907/mirri/hhc8bj
title: MIRRI0121866

description: Organism type: Filamentous Fungi ; Taxon name: Xylaria longipes ; Collection: MUCL 29026 ; Country: Belgium
DOI: 10.57907/mirri/j5grdg
title: MIRRI0122015

description: Organism type: Yeast ; Taxon name: Saccharomyces cerevisiae ; Collection: MUCL 29248 ; Country: Belgium
DOI: 10.57907/mirri/jlmnb6
title: MIRRI0121607

description: Organism type: Yeast ; Taxon name: Rhodosporidium toruloides ; Collection: MUCL 28637 ; Country: Sweden
DOI: 10.57907/mirri/jlmnb6/cjpse1
title: MIRRI0121607.json

description: Strain json file
DOI: 10.57907/mirri/lrc5wu
title: MIRRI0121970

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium aurantiogriseum var. aurantiogriseum ; Collection: MUCL 29179
DOI: 10.57907/mirri/mwlqsa/hg4iwn
title: MIRRI0121901.json

description: Strain json file
DOI: 10.57907/mirri/ngbrsv
title: MIRRI0121732

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium brevicompactum ; Collection: MUCL 28813
DOI: 10.57907/mirri/odv384
title: MIRRI0121941

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium rubens ; Collection: MUCL 29139 ; Country: Belgium
DOI: 10.57907/mirri/ofkqpv/txmjtc
title: MIRRI0121907.json

description: Strain json file
DOI: 10.57907/mirri/otsffl
title: MIRRI0121630

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium aurantiogriseum var. aurantiogriseum ; Collection: MUCL 28660
DOI: 10.57907/mirri/rxjvzd/94y727
title: MIRRI0121613.json

description: Strain json file
DOI: 10.57907/mirri/ux8rrb
title: MIRRI0121959

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium jensenii ; Collection: MUCL 29168 ; Country: Poland
DOI: 10.57907/mirri/vaudby/sadbko
title: MIRRI0121664.json

description: Strain json file
DOI: 10.57907/mirri/wbuljh/k4qayx
title: MIRRI0121983.json

description: Strain json file
DOI: 10.57907/mirri/wvecov/uisc6n
title: MIRRI0121621.json

description: Strain json file
DOI: 10.3535/5x9-czf-gvb
title: Lolium perenne L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/nkc-7fm-6cj
title: Bunium paucifolium DC.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/2culo3
title: MIRRI0119372

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus sydowii ; Collection: MUCL 14405 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/4thysd
title: MIRRI0121971

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium solitum ; Collection: MUCL 29183
DOI: 10.57907/mirri/54g0am
title: MIRRI0119389

description: Organism type: Filamentous Fungi ; Taxon name: Trichocladium griseum ; Collection: MUCL 14438 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/acungt
title: MIRRI0121974

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium verrucosum ; Collection: MUCL 29186 ; Country: Belgium
DOI: 10.57907/mirri/bfntln
title: MIRRI0121911

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium verrucosum ; Collection: MUCL 29089
DOI: 10.57907/mirri/cxzoom/vnu7mi
title: MIRRI0122001.json

description: Strain json file
DOI: 10.57907/mirri/e05ax9/ug7rdi
title: MIRRI0119398.json

description: Strain json file
DOI: 10.57907/mirri/ffpajz/mruprk
title: MIRRI0121928.json

description: Strain json file
DOI: 10.57907/mirri/fiskmg
title: MIRRI0122046

description: Organism type: Filamentous Fungi ; Taxon name: Eurotium rubrum ; Collection: MUCL 29286
DOI: 10.57907/mirri/i3ssxj
title: MIRRI0119418

description: Organism type: Yeast ; Taxon name: Trichosporon dulcitum ; Collection: MUCL 14483
DOI: 10.57907/mirri/inpdye
title: MIRRI0121946

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium roqueforti ; Collection: MUCL 29150
DOI: 10.57907/mirri/itteva
title: MIRRI0121985

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium hirsutum ; Collection: MUCL 29205
DOI: 10.57907/mirri/ndvyix/syrpdm
title: MIRRI0119382.json

description: Strain json file
DOI: 10.57907/mirri/rgxhj3
title: MIRRI0122055

description: Organism type: Filamentous Fungi ; Taxon name: Mucor racemosus f. racemosus ; Collection: MUCL 29302 ; Country: Switzerland
DOI: 10.57907/mirri/roc19t
title: MIRRI0119413

description: Organism type: Yeast ; Taxon name: Trichosporon inkin ; Collection: MUCL 14476 ; Country: Portugal
DOI: 10.57907/mirri/ruu3un
title: MIRRI0122022

description: Organism type: Filamentous Fungi ; Taxon name: Pseudallescheria boydii ; Collection: MUCL 29252 ; Country: Democratic Republic of the Congo
DOI: 10.57907/mirri/rz32qz
title: MIRRI0121950

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium aurantiogriseum var. aurantiogriseum ; Collection: MUCL 29155 ; Country: France
DOI: 10.57907/mirri/vpxqvu
title: MIRRI0122013

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium raciborskii ; Collection: MUCL 29246 ; Country: Poland
DOI: 10.57907/mirri/znw3ef
title: MIRRI0121938

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium corylophilum ; Collection: MUCL 29131
DOI: 10.3535/9a5-5ay-1ws
title: Galium verum subsp. verum

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/e0l-ztj-w7a
title: Plantago uliginosa subsp. uliginosa

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.5281/zenodo.15719994
title: DaphnAI: A Deep Learning Approach for High-Throughput Zooplankton Community Analysis

description: Contents





dataset.zip

A compressed folder that contains:





images/: Raw image data used for training and validation and testing.




labels/: YOLO-format .txt annotation files for the corresponding images.




out/: Images annotated with segmentation polygons and class labels, useful for visualization and quality control.






trainer.sh

A shell script to initiate YOLOv12 model training. It configures the dataset, model architecture, and training hyperparameters.




data_species.yaml

YAML file specifying dataset structure and class labels. It defines 7 classes:

["D_pulex", "ballooned", "copepod", "egg", "resting_egg", "D_galeata", "S_vetulus"].




chunker.py

A utility script for preprocessing high-resolution images. It splits large images into chunks for more effective training on high-resolution biological data. Supports .tif, .png, and .jpg formats.




d_pulex_missclass_analysis.ipynb

A Jupyter notebook used for post-training analysis, focusing on the misclassification of Daphnia pulex.




 
autosplit_train_res.csvA csv file containing the inference results of the test images (used for the analysis of misclassification of Daphnia pulex)



DaphnAI.pt



           The weights of the model (pre trained-model).





Interactive Jupyter tutorial (tutorial.ipynb)



           A step-by-step notebook for inference, visualization, and data extraction with code and explanations.
DOI: 10.5281/zenodo.15719995
title: DaphnAI: A Deep Learning Approach for High-Throughput Zooplankton Community Analysis

description: Contents





dataset.zip

A compressed folder that contains:





images/: Raw image data used for training and validation and testing.




labels/: YOLO-format .txt annotation files for the corresponding images.




out/: Images annotated with segmentation polygons and class labels, useful for visualization and quality control.






trainer.sh

A shell script to initiate YOLOv12 model training. It configures the dataset, model architecture, and training hyperparameters.




data_species.yaml

YAML file specifying dataset structure and class labels. It defines 7 classes:

["D_pulex", "ballooned", "copepod", "egg", "resting_egg", "D_galeata", "S_vetulus"].




chunker.py

A utility script for preprocessing high-resolution images. It splits large images into chunks for more effective training on high-resolution biological data. Supports .tif, .png, and .jpg formats.




d_pulex_missclass_analysis.ipynb

A Jupyter notebook used for post-training analysis, focusing on the misclassification of Daphnia pulex.




 
autosplit_train_res.csvA csv file containing the inference results of the test images (used for the analysis of misclassification of Daphnia pulex)



DaphnAI.pt



           The weights of the model (pre trained-model).





Interactive Jupyter tutorial (tutorial.ipynb)



           A step-by-step notebook for inference, visualization, and data extraction with code and explanations.
DOI: 10.57907/mirri/57o4kq
title: MIRRI0122008

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium roseopurpureum ; Collection: MUCL 29237 ; Country: Belgium
DOI: 10.57907/mirri/9uddhi
title: MIRRI0122060

description: Organism type: Filamentous Fungi ; Taxon name: Cochliobolus sativus ; Collection: MUCL 2935 ; Country: Canada
DOI: 10.57907/mirri/bhbluo/cswb3d
title: MIRRI0122004.json

description: Strain json file
DOI: 10.57907/mirri/l0qvev/cgz8ry
title: MIRRI0122020.json

description: Strain json file
DOI: 10.57907/mirri/ua79qt
title: MIRRI0122032

description: Organism type: Filamentous Fungi ; Taxon name: Pseudallescheria boydii ; Collection: MUCL 29257 ; Country: Belgium
DOI: 10.57907/mirri/x2ryfz/cnfaps
title: MIRRI0122033.json

description: Strain json file
DOI: 10.3535/ads-0my-tgg
title: Lophopterys occidentalis W. R. Anderson & C. Davis

description: Digital Specimen for the physical specimen hosted at University of Graz.