Published December 15, 2025
| Version v1
Journal article
Open
A digitization workflow of dry-pinned collections of Lepidoptera
Authors/Creators
- 1. University of Florida, Gainesville, United States of America
Description
Butterflies and moths (Lepidoptera) are one of the most commonly found insect groups in museum collections. Yet many specimens still lack digital data and few digitization workflows are available. Here we present a digitization workflow for natural history collections that can be widely applicable for any museum or dried pinned-specimen collection of Lepidoptera. Our workflow consists of pre-imaging preparation, usage of a copy stand for imaging pinned specimens and data labels, image processing, and transcription, the latter two which utilize Python scripts for optimization.
Files
ZK_article_134756.pdf
Files
(3.6 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:134176f9ab1844af8c3e79cfa7dbe4cd
|
3.6 MB | Preview Download |
System files
(142.5 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:715d09b76ef4a5bbfee1edb5987da369
|
142.5 kB | Download |
Linked records
Additional details
References
- Aiello BR, Sikandar UB, Minoguchi H, Bhinderwala B, Hamilton CA, Kawahara AY, Sponberg S (2021) The evolution of two distinct strategies of moth flight. Journal of the Royal Society, Interface 18(185): e20210632. https://doi.org/10.1098/rsif.2021.0632
- Almryad AS, Kutucu H (2020) Automatic identification for field butterflies by convolutional neural networks. Engineering Science and Technology, an International Journal 23(1): 189–195. https://doi.org/10.1016/j.jestch.2020.01.006
- Ball-Damerow JE, Brenskelle L, Barve N, Soltis PS, Sierwald P, Bieler R, LaFrance R, Ariño AH, Guralnick RP (2019) Research applications of primary biodiversity databases in the digital age. PLoS ONE 14(9): e0215794. https://doi.org/10.1371/journal.pone.0215794
- Bedford FE, Whittaker RJ, Kerr JT (2012) Systemic range shift lags among a pollinator species assemblage following rapid climate change. Botany 90(7): 587–597. https://doi.org/10.1139/b2012-052
- Belitz MW, Larsen EA, Shirey V, Li D, Guralnick RP (2023) Phenological research based on natural history collections: Practical guidelines and a lepidopteran case study. Functional Ecology 37(2): 234–247. https://doi.org/10.1111/1365-2435.14173
- Bertone MA, Blinn RL, Stanfield TM, Dew KJ, Seltmann KC, Deans AR (2012) Results and insights from the NCSU Insect Museum GigaPan project. ZooKeys 209: 115–132. https://doi.org/10.3897/zookeys.209.3083
- Blagoderov V, Kitching IJ, Livermore L, Simonsen TJ, Smith VS (2012) No specimen left behind: Industrial scale digitization of natural history collections. ZooKeys 209: 133–146. https://doi.org/10.3897/zookeys.209.3178
- Blagoderov V, Penn M, Sadka M, Hine A, Brooks S, Siebert DJ, Sleep C, Cafferty S, Cane E, Martin G, Toloni F, Wing P, Chainey J, Duffell L, Huxley R, Ledger S, McLaughlin C, Mazzetta G, Perera J, Crowther R, Douglas L, Durant J, Honey M, Huertas B, Howard T, Carter V, Albuquerque S, Paterson G, Kitching IJ (2017) iCollections methodology: Workflow, results and lessons learned. Biodiversity Data Journal 19893: e19893. https://doi.org/10.3897/BDJ.5.e19893
- Brown J (2012) ZBar. https://github.com/ZBar/ZBar [accessed 12 June 2019]
- Buschbacher K, Ahrens D, Espeland M, Steinhage V (2020) Image-based species identification of wild bees using convolutional neural networks. Ecological Informatics 55: e101017. https://doi.org/10.1016/j.ecoinf.2019.101017
- Caspers M, Willemse L, Miracle EG, van Nieukerken EJ (2019) Butterflies in bags: Permanent storage of Lepidoptera in glassine envelopes. Nota Lepidopterologica 42(1): 1–16. https://doi.org/10.3897/nl.42.28654
- Chan W-P, Childers RR, Ashe S, Tsai C-C, Elson C, Keleher KJ, Sipe RLH, Maier CA, Sourakov A, Gall LF, Bernard GD, Soucy ER, Yu N, Pierce NE (2022) A high-throughput multispectral imaging system for museum specimens. Communications Biology 5(1): e1318. https://doi.org/10.1038/s42003-022-04282-z
- Childers RR, Cai L, Chowdhury S, Crall J, Cornwall M, Sipe RH, Maier C, Maunsell S, Talavera G, Tsai C-C, Angier K, Barve V, Dankowicz E, Hinolan J, Itliong M, Naive MA, Johnson G, Matos F, Morgan V, Plotkin D, Salcedo M, Shirey V, Vermilya K, Winstanley J, Wu A, Guralnick R, Kawahara A, Lohman D, Ries L, Soucy E, Vila R, Yu N, Pierce N, Chan W-P (2023) Selection on size has generated distinctive paired wing flight systems for butterfly flight and migration. https://doi.org/10.21203/rs.3.rs-2968821/v1
- Clark JA (2021) Pillow (PIL Fork) 8.2.0. https://pypi.org/project/Pillow/8.2.0/ [accessed 12 June 2019]
- Cobb NS, Gall LF, Zaspel JM, Dowdy NJ, McCabe LM, Kawahara AY (2019) Assessment of North American arthropod collections: Prospects and challenges for addressing biodiversity research. PeerJ 7: e8086. https://doi.org/10.7717/peerj.8086
- Cunha C, Narotamo H, Monteiro A, Silveira M (2023) Detection and measurement of butterfly eyespot and spot patterns using convolutional neural networks. PLoS ONE 18(2): e0280998. https://doi.org/10.1371/journal.pone.0280998
- Delpeuch A, Morris T, Huynh D, Weblate Mazzocchi S, Jacky Guidry T, elebitzero Stephens O, Matsunami I, Sproat I, Larsson A, Santos S, allanaaa kushthedude , Fauconnier S, Mishra E, Magdinier M, Beaubien A, Liu L, Giroud F, Ong J, Tacchelli F, Nordhøy A, Luca Martinelli [Sannita], Kanye E, Saby M, Chandra L (2024) OpenRefine/OpenRefine: OpenRefine v3.8-beta1. https://zenodo.org/records/10689569 [accessed 20 October 2025]
- DeWalt R, Yoder M, Snyder E, Dmitriev D, Ower G (2018) Wet collections accession: A workflow based on a large stonefly (Insecta, Plecoptera) donation. Biodiversity Data Journal 6: e30256. https://doi.org/10.3897/BDJ.6.e30256
- Dupont S, Humphries J, Butcher A, Baker E, Balcells L, Price B (2020) Ahead of the curve: Three approaches to mass digitisation of vials with a focus on label data capture. Research Ideas and Outcomes 6: e53606. https://doi.org/10.3897/rio.6.e53606
- Earl C, Belitz MW, Laffan SW, Barve V, Barve N, Soltis DE, Allen JM, Soltis PS, Mishler BD, Kawahara AY, Guralnick R (2021) Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America. iScience 24(4): e102239. https://doi.org/10.1016/j.isci.2021.102239
- Echevarría Ramos M, Hulshof CM (2019) Using digitized museum collections to understand the effects of habitat on wing coloration in the Puerto Rican monarch. Biotropica 51(4): 477–483. https://doi.org/10.1111/btp.12680
- Entomology Collection Network (2023) BugFlow. https://github.com/EntCollNet/BugFlow [accessed 13 November 2023]
- GBIF (2024) The Global Biodiversity Information Facility What is GBIF? https://www.gbif.org/what-is-gbif [accessed 20 September 2024]
- Giribet G, Edgecombe GD (2012) Reevaluating the arthropod tree of life. Annual Review of Entomology 57(1): 167–186. https://doi.org/10.1146/annurev-ento-120710-100659
- Guralnick R, LaFrance R, Denslow M, Blickhan S, Bouslog M, Miller S, Yost J, Best J, Paul DL, Ellwood E, Gilbert E, Allen J (2024) Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks. Applications in Plant Sciences 12(1): e11560. https://doi.org/10.1002/aps3.11560
- Hamilton CA, Winiger N, Rubin JJ, Breinholt J, Rougerie R, Kitching IJ, Barber JR, Kawahara AY (2022) Hidden phylogenomic signal helps elucidate Arsenurine silkmoth phylogeny and the evolution of body size and wing shape trade-offs. Systematic Biology 71(4): 859–874. https://doi.org/10.1093/sysbio/syab090
- Harris KM, Marsico TD (2017) Digitizing specimens in a small herbarium: A viable workflow for collections working with limited resources. Applications in Plant Sciences 5(4): e1600125. https://doi.org/10.3732/apps.1600125
- Hedrick BP, Heberling JM, Meineke EK, Turner KG, Grassa CJ, Park DS, Kennedy J, Clarke JA, Cook JA, Blackburn DC, Edwards SV, Davis CC (2020) Digitization and the future of natural history collections. Bioscience 70(3): 243–251. https://doi.org/10.1093/biosci/biz163
- Herbst R, Stille D, Gwilliam GF, Von Konrat M, Campbell T, Gaswick W, Grewe F, Hansen K, Iacobelli F, Jellema K, Kawasaki ML, Kreider D, Ree RH, Rodriguez Y, Wolpert A (2025) Unlocking the Past: The Potential of Large Language Models to Revolutionize Transcription of Natural History Collections. Data Intelligence 7(2): 237–264. https://doi.org/10.3724/2096-7004.di.2025.0011
- Hereld M, Ferrier N (2019) LightningBug ONE: An experiment in high-throughput digitization of pinned insects. Biodiversity Information Science and Standards 3: e37228. https://doi.org/10.3897/biss.3.37228
- Hereld M, Ferrier NJ, Agarwal N, Sierwald P (2017) Designing a High-Throughput Pipeline for Digitizing Pinned Insects. 2017 IEEE 13th International Conference on e-Science (e-Science). IEEE, Auckland, 542–550. https://doi.org/10.1109/eScience.2017.88
- Hill A, Guralnick R, Smith A, Sallans A, Gillespie R, Denslow M, Gross J, Murrell Z, Conyers T, Oboyski P, Ball J, Thomer A, Prys-Jones R, De La Torre J, Kociolek P, Fortson L (2012) The notes from nature tool for unlocking biodiversity records from museum records through citizen science. ZooKeys 209: 219–233. https://doi.org/10.3897/zookeys.209.3472
- Holmes MW, Hammond TT, Wogan GOU, Walsh RE, LaBarbera K, Wommack EA, Martins FM, Crawford JC, Mack KL, Bloch LM, Nachman MW (2016) Natural history collections as windows on evolutionary processes. Molecular Ecology 25(4): 864–881. https://doi.org/10.1111/mec.13529
- Homziak NT (2022) Evolution of hindwing color in underwing moths. PhD Thesis, University of Florida, Gainesville, Florida, United States.
- Hudson LN, Blagoderov V, Heaton A, Holtzhausen P, Livermore L, Price BW, van der Walt S, Smith VS (2015) Inselect: Automating the digitization of natural history collections. PLoS ONE 10(11): e0143402. https://doi.org/10.1371/journal.pone.0143402
- iDigBio.org (2024) iDigBio Home Page. https://www.idigbio.org/ [accessed 20 September 2024]
- Kawahara AY, Emmel TC, Miller J, Warren AD (2012) A new institution devoted to insect science: The Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity. Insect Science 19(3): 426–428. https://doi.org/10.1111/j.1744-7917.2011.01490.x
- Kharouba HM, Lewthwaite JMM, Guralnick R, Kerr JT, Vellend M (2019) Using insect natural history collections to study global change impacts: Challenges and opportunities. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 374(1763): e20170405. https://doi.org/10.1098/rstb.2017.0405
- Leopold A (2021) FLMNH-MGCL/datamatrix: v0.1.0. https://doi.org/10.5281/zenodo.4829080 [accessed 15 February 2025]
- Leopold A, O'Connell M (2023) FLMNH-MGCL/digitization: 0.0.1. https://zenodo.org/records/10032175 [accessed 15 February 2025]
- Li D, Stucky BJ, Deck J, Baiser B, Guralnick RP (2019) The effect of urbanization on plant phenology depends on regional temperature. Nature Ecology & Evolution 3(12): 1661–1667. https://doi.org/10.1038/s41559-019-1004-1
- Mantle B, LaSalle J, Fisher N (2012) Whole-drawer imaging for digital management and curation of a large entomological collection. ZooKeys 209: 147–163. https://doi.org/10.3897/zookeys.209.3169
- May KJ, Ristaino JB (2004) Identity of the mtDNA haplotype(s) of Phytophthora infestans in historical specimens from the Irish Potato Famine. Mycological Research 108(5): 471–479. https://doi.org/10.1017/S0953756204009876
- Mendez PK, Lee S, Venter CE (2018) Imaging natural history museum collections from the bottom up: 3D print technology facilitates imaging of fluid-stored arthropods with flatbed scanners. ZooKeys 795: 49–65. https://doi.org/10.3897/zookeys.795.28416
- Misbakh-Soloviov VA (2016) dmtx/dmtx-utils. https://github.com/dmtx/dmtx-utils [accessed 11 June 2019]
- Nelson G, Ellis S (2018) The history and impact of digitization and digital data mobilization on biodiversity research. Philosophical Transactions of the Royal Society B 374(1763): e20170391. https://doi.org/10.1098/rstb.2017.0391
- Nelson G, Paul D, Riccardi G, Mast AR (2012) Five task clusters that enable efficient and effective digitization of biological collections. ZooKeys 209: 19–45. https://doi.org/10.3897/zookeys.209.3135
- Nelson G, Sweeney P, Wallace LE, Rabeler RK, Allard D, Brown H, Carter JR, Denslow MW, Ellwood ER, Germain‐Aubrey CC, Gilbert E, Gillespie E, Goertzen LR, Legler B, Marchant DB, Marsico TD, Morris AB, Murrell Z, Nazaire M, Neefus C, Oberreiter S, Paul D, Ruhfel BR, Sasek T, Shaw J, Soltis PS, Watson K, Weeks A, Mast AR (2015) Digitization workflows for flat sheets and packets of plants, algae, and fungi. Applications in Plant Sciences 3(9): e1500065. https://doi.org/10.3732/apps.1500065
- Ortiz-Acevedo E, Gomez JP, Espeland M, Touissaint EFA, Willmott KR (2020) The roles of wing color pattern and geography in the evolution of Neotropical Preponini butterflies. Ecology and Evolution 23(23): 12801–12816. https://doi.org/10.1002/ece3.6816
- Owens HL, Lewis DS, Condamine FL, Kawahara AY, Guralnick RP (2020) Comparative Phylogenetics of Papilio butterfly wing shape and size demonstrates independent hindwing and forewing evolution. Systematic Biology 69(5): 813–819. https://doi.org/10.1093/sysbio/syaa029
- Paterson G, Albuquerque S, Blagoderov V, Brooks S, Cafferty S, Cane E, Carter V, Chainey J, Crowther R, Douglas L, Durant J, Duffell L, Hine A, Honey M, Huertas B, Howard T, Huxley R, Kitching I, Ledger S, McLaughlin C, Martin G, Mazzetta G, Penn M, Perera J, Sadka M, Scialabba E, Self A, Siebert DJ, Sleep C, Toloni F, Wing P (2016) iCollections – Digitising the British and Irish Butterflies in the Natural History Museum, London. Biodiversity Data Journal 9559: e9559. https://doi.org/10.3897/BDJ.4.e9559
- Popkov A, Konstantinov F, Neimorovets V, Solodovnikov A (2022) Machine learning for expert‐level image‐based identification of very similar species in the hyperdiverse plant bug family Miridae (Hemiptera: Heteroptera). Systematic Entomology 47(3): 487–503. https://doi.org/10.1111/syen.12543
- Qin W, Abbas A, Abbas S, Alam A, Chen D, Hafeez F, Ali J, Romano D, Chen R-Z (2024) Automated lepidopteran pest developmental stages classification via transfer learning framework. Environmental Entomology 53(6): 1062–1077. https://doi.org/10.1093/ee/nvae085
- Schmidt S, Balke M, Lafogler S (2012) DScan – a high-performance digital scanning system for entomological collections. ZooKeys 209: 183–191. https://doi.org/10.3897/zookeys.209.3115
- Seltmann KC, Cobb NS, Gall LF, Bartlett CR, Basham MA, Betancourt I, Bills C, Brandt B, Brown RL, Bundy C, Caterino MS, Chapman C, Cognato A, Colby J, Cook SP, Daly KM, Dyer LA, Franz NM, Gelhaus JK, Grinter CC, Harp CE, Hawkins RL, Heydon SL, Hill GM, Huber S, Johnson N, Kawahara AY, Kimsey LS, Kondratieff BC, Krell F-T, Leblanc L, Lee S, Marshall CJ, Mccabe LM, Mchugh JV, Menard KL, Opler PA, Palffy-Muhoray N, Pardikes N, Peterson MA, Pierce NE, Poremski A, Sikes DS, Weintraub JD, Wikle D, Zaspel JM, Zolnerowich G (2017) LepNet: The Lepidoptera of North America Network. Zootaxa 4247(1): 73–77. https://doi.org/10.11646/zootaxa.4247.1.10
- Short AEZ, Dikow T, Moreau CS (2018) Entomological collections in the age of big data. Annual Review of Entomology 63(1): 513–530. https://doi.org/10.1146/annurev-ento-031616-035536
- Takano A, Horiuchi Y, Fujimoto Y, Aoki K, Mitsuhashi H, Takahashi A (2019) Simple but long-lasting: A specimen imaging method applicable for small- and medium-sized herbaria. PhytoKeys 118: 1–14. https://doi.org/10.3897/phytokeys.118.29434
- Tegelberg R, Mononen T, Saarenmaa H (2014) High‐performance digitization of natural history collections: Automated imaging lines for herbarium and insect specimens. Taxon 63(6): 1307–1313. https://doi.org/10.12705/636.13
- Tegelberg R, Kahanpaa J, Karppinen J, Mononen T, Wu Z, Saarenmaa H (2017) Mass Digitization of Individual Pinned Insects Using Conveyor-Driven Imaging. 2017 IEEE 13th International Conference on e-Science (e-Science). IEEE, Auckland, 523–527. https://doi.org/10.1109/eScience.2017.85
- Terry CN, Alonso‐Rodríguez AM, Miller SE, Hulshof CM (2023) Lepidoptera research in Puerto Rico: Reconnecting with historical legacies to guide future priorities. Biotropica 55(6): 1215–1232. https://doi.org/10.1111/btp.13278
- Thiers BM, Tulig MC, Watson KA (2016) Digitization of The New York Botanical Garden Herbarium. Brittonia 68(3): 324–333. https://doi.org/10.1007/s12228-016-9423-7
- Van Rossum G, Drake FL (2009) Python 3 Reference Manual. CreateSpace, Scotts Valley, California, 242 pp.
- Wells CN, Tonkyn DW (2014) Range collapse in the Diana fritillary, Speyeria diana (Nymphalidae). Insect Conservation and Diversity 7(4): 365–380. https://doi.org/10.1111/icad.12059