Проста й недорога фотосистема для оцифрування гербарію
The digitization of the natural history collections is a crucial task of today. It allows not only sharing the data but also virtually preserving the specimens. This is especially important for small collections that suffer from limited financial support and can be easily lost. Here we share our exp...
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2021
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| author | Novikov, Andriy Sup-Novikova, Mariia |
| author_facet | Novikov, Andriy Sup-Novikova, Mariia |
| author_sort | Novikov, Andriy |
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| description | The digitization of the natural history collections is a crucial task of today. It allows not only sharing the data but also virtually preserving the specimens. This is especially important for small collections that suffer from limited financial support and can be easily lost.
Here we share our experience of the building of cheap and simple photosystem that can be used for routine digitization of local herbaria with low or without incomes. This photosystem is modular and based on the regular components that can be easily purchased and/or updated. It is compact and can be conveniently assembled and disassembled, and transported. This photosystem consists of horizontal tripod Beike Q999H with two led lamps Yongnuo YN-300 Air mounted on the 11” Magic Arm handles. The camera Canon EOS 800D was chosen due to presence of fully rotated display, the high resolution, modern focusing system, RAW format support, and low price on the market. The lens Tokina AT-X M35 PRO DX AF 35 mm f/2.8 Macro was chosen due to extreme sharpness along the whole capturing field, low aberrations and optical distortion, high light sensitivity, and fast autofocus.
We also tested light box as an option for herbarium specimens’ digitization. However, we found that light box is inconvenient for herbarium digitization dues several reasons, among which its massive sizes, limited access to working space, and necessity of application of huge mounting system that should hold the camera far higher over the center of light box. In general, work with light box significantly decelerated the digitization process. We did not find any advantaged in use of the light box and therefore it was rejected. We hope that our experience will be useful for other curators wanting to digitize their collections and having limited budget. |
| doi_str_mv | 10.46341/PI2021015 |
| first_indexed | 2025-07-17T12:54:02Z |
| format | Article |
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© The Authors. This content is provided under CC BY 4.0 license.
Plant Introduction, 91/92, 50–53 (2021)
SHORT COMMUNICATION
Simple and cheap photosystem for herbarium digitization
Andriy Novikov 1, Mariia Sup-Novikova 2
1 State Museum of Natural History, National Academy of Sciences of Ukraine, Teatralna str. 18, 79008 Lviv, Ukraine;
novikoffav@gmail.com
2 Ukrainian Catholic University, Stryiska str. 29A, 79026 Lviv, Ukraine
Received: 21.11.2021 | Accepted: 12.12.2021 | Published online: 14.12.2021
Abstract
The digitization of the natural history collections is a crucial task of today. It allows not only sharing the
data but also virtually preserving the specimens. This is especially important for small collections that
suffer from limited financial support and can be easily lost.
Here we share our experience of the building of cheap and simple photosystem that can be used for
routine digitization of local herbaria with low or without incomes. This photosystem is modular and
based on the regular components that can be easily purchased and/or updated. It is compact and can
be conveniently assembled and disassembled, and transported. This photosystem consists of horizontal
tripod Beike Q999H with two led lamps Yongnuo YN-300 Air mounted on the 11” Magic Arm handles. The
camera Canon EOS 800D was chosen due to presence of fully rotated display, the high resolution, modern
focusing system, RAW format support, and low price on the market. The lens Tokina AT-X M35 PRO DX AF
35 mm f/2.8 Macro was chosen due to extreme sharpness along the whole capturing field, low aberrations
and optical distortion, high light sensitivity, and fast autofocus.
We also tested light box as an option for herbarium specimens’ digitization. However, we found that
light box is inconvenient for herbarium digitization dues several reasons, among which its massive sizes,
limited access to working space, and necessity of application of huge mounting system that should hold
the camera far higher over the center of light box. In general, work with light box significantly decelerated
the digitization process. We did not find any advantaged in use of the light box and therefore it was
rejected. We hope that our experience will be useful for other curators wanting to digitize their collections
and having limited budget.
Keywords: herbarium, digitization, small collections, photosystem construction
https://doi.org/10.46341/PI2021015
UDC 58.086
Authors’ contributions: Novikov A. designed a photosystem and organized the digitization process, and prepared the manuscript.
Sup-Novikova M. tested the photosystem, assisted during the digitization, and corrected the manuscript.
Funding: The photosystem for the herbarium digitization was built on the costs of the IAPT Small Collections Grant received by
Novikov A. in 2021.
Competing Interests: The authors declare no conflict of interest.
Even today, when modern communication
technologies and international transportation
system are well developed, many natural
history collections remain hidden from
scientific community or have limited access
due to different reasons. Among the modern
https://creativecommons.org/licenses/by/4.0/
https://orcid.org/0000-0002-0112-5070
https://orcid.org/0000-0002-8542-3605
Plant Introduction • 91/92 51
Simple and cheap photosystem for herbarium digitization
challenges, restricting the access to natural
history collections is COVID-19 pandemic
(Baker, 2020). For example, the access to
the one of the most valuable collections in
Ukraine, the Herbarium of the Ivan Franko
National University of Lviv (LW), is fully
forbidden for last two years. The access to the
biggest herbarium in Ukraine hosted at the
M.G. Kholodny Institute of Botany of the NAS
of Ukraine (KW) was strongly limited during
2020–2021. Due to pandemic limitations, travel
to other countries today can be complicated,
what makes access to other collections also
questionable.
While the biggest herbaria are, depending
on the country, more or less digitized, small
collections in many cases are still poorly
represented in the databases. At the same
time, small herbaria are the most vulnerable
due to limited financial support and can be
easily lost. Therefore, digitization of such
small herbaria is a crucial task providing many
research benefits (Holovachov et al., 2014;
Cantrill, 2018) and allowing virtually preserve
them (Novikov, 2019).
One of such vulnerable collections is
the Herbarium of the State Museum of
the Natural History of the NAS of Ukraine
(LWS) hosting about 118K specimens. This is
not a small herbarium in a strict sense, but
rather a local one (Bridson & Forman, 2013)
covering mostly western part of Ukraine,
and representing especially the flora of the
Ukrainian Carpathians. Taking into account
extremely low budget of our herbarium, it was
not possible to purchase such professional
digitization solutions as Picturae or Microtek
ObjectScan. Therefore, under support of the
IAPT Small Collections Grant and considering
the recommendations of Takano et al. (2019)
we built the simple and cheap photosystem
that can be easily applied for routine
digitization of the herbarium specimens. Our
main requirements to the photosystem were:
(1) use of on-the-market components that
can be easily purchased and/or updated;
(2) modularity, allowing fast replacement of the
elements; (3) small size allowing comfortable
work in the limited working space.
Fist we tried to use a light box PULUZ
PU5060, however very soon we found several
critical disadvantages of such solution. First, it
is problematic to manipulate with herbarium
sheets because only front part of the light
box is open – this significantly slower the
digitization process. Second, light box does
not allow using standard horizontal tripod,
because the upper hole is located too far and
cannot be reached by normal tripod arm. As
a result, it is necessary to build a huge and
static mounting system that is expensive
and faintly mobile. Third, in case of light box
application, the camera appears relatively
high and requires use of specific lenses. In
particular, we found that sharpness of our lens
(i.e., Tokina AT-X M35 PRO DX AF 35 mm f/2.8
Macro) significantly decreased with increased
distance from the operating surface. Finally,
use of the light box in general requires much
more working space.
Therefore, we took our second attempt and
decided to renounce the light box application.
Instead of this, we built the photosystem
basing on the standard horizontal tripod
Beike Q999H (Fig. 1A). As a light source, we
applied two led lamps Yongnuo YN-300 Air
with regulated illumination and two color
temperature regimes (3200 and 5600K). The
lamps were mounted directly on the tripod’s
legs using two 11” Magic Arm handles. The
lamps were adjusted to 5600K-only regime
with 60% of intensity. We also tested use
of different light combinations (i.e., with
additional diffuse natural (upper left corner)
and ceiling light (6400K), with additional
ceiling light only, and with additional diffuse
natural light only). However, this did not
influence significantly the quality of obtained
results. Influence of a direct natural light was
not tested due to absence of such illumination
in a working room (windows are located in
such a way that strong direct light did not
reach the room). Over all, we found that two
Yongnuo YN-300 lamps without any additional
illumination are enough to obtain adequate
results. Just to isolate the photographic area
from other room space we installed the mat-
white MDF board after the tripod. The tripod
was placed over the cutting mat Axent Pro A3.
Additionally, for further image calibration
and processing, we applied a ruler with official
herbarium logo and X-rite ColorChecker
Classic Mini (Fig. 1B). ColorChecker allows
calibrating the color balance and white
balance, so this also helps to reduce the
slightly disproportionate illumination obtained
during different working hours. It is preferable
to use X-rite ColorChecker Classic Nano,
52 Plant Introduction • 91/92
A. Novikov, M. Sup-Novikova
which is only 22 × 36 mm in size. It is more
suitable for herbarium digitization because it
does not overlap the specimens so much as
X-rite ColorChecker Classic Mini (57 × 86 mm).
However, the price for the smallest version of
ColorChecker is almost three times higher,
which can be a key decision point if the budget
is limited.
We would prefer to use a full-frame camera,
but due the limited costs, we choose cropped
Canon EOS 800D. The reasons why we
chose this camera were: (a) presence of fully
rotated display, which is necessary during the
horizontal photographing; (b) the high enough
resolution (24.2 Mpx); (c) focusing system with
45 focus points allowing quick image capture;
(d) RAW format support; (e) low price on the
market. The choice of the lens was not so easy.
We experimented with zoom (Canon EF-S 18-
135 mm f/3.5-5.6 IS STM) regular prime (Canon
EF 50 mm f/1.4 USM) and macro prime (Canon
EF 100 mm f/2.8 Macro USM and Tokina AT-X
M35 PRO DX AF 35 mm f/2.8 Macro) lenses.
We found that macro lenses produced the
sharpest images, while the 35 mm and 50 mm
lenses had the lowest optical distortion.
Finally, we chose Tokina 35 mm macro lens
that also demonstrated low image aberrations,
brilliant image sharpness on its whole field,
and had two focusing regimes allowing faster
picture capturing.
In a result, we obtained a cheap (the whole
photosystem costed about 1325 Euros) and
easy to use photosystem that can be quickly
rebuild or updated, and produces images
of high quality. This photosystem can be
also easily assembled and disassembled,
transported, and do not occupy much of
working space. Application of tripod simplify
the manipulations with herbarium vouchers,
because there is no walls limiting the access.
We hope that our experience will be useful
for other curators wanting to digitize their
collections and having limited budget.
Acknowledgements
We thank IAPT for providing AN the Small
Collections Grant that allowed to start
Figure 1. A common view of the photosystem (A) and an example of obtained picture (B).
A B
Plant Introduction • 91/92 53
Simple and cheap photosystem for herbarium digitization
Проста й недорога фотосистема для оцифрування гербарію
Андрій Новіков 1, Марія Суп-Новікова 2
1 Державний природознавчий музей НАН України, вул. Театральна, 18, Львів, 79008, Україна;
novikoffav@gmail.com
2 Український католицький університет, вул. Стрийська, 29А, Львів, 79026, Україна
Оцифрування природничих колекцій на сьогодні постає надзвичайно важливим питанням, яке
дозволяє не лише поширювати отримані дані, але й віртуально зберігати зразки. Це особливо
важливо для малих колекцій, які регулярно потерпають від недофінансування і можуть бути легко
втрачені.
В цій публікації ми ділимося досвідом побудови дешевої і простої фотосистеми, що може
використовуватися для рутинного оцифрування локальних гербаріїв, які мають обмежений бюджет
або й опинилися без фінансової підтримки взагалі. Ця фотосистема є модульною і побудована на
звичних компонентах, які можна легко придбати та/або вдосконалити. Вона є компактною, зручно
складається і розкладається, а також транспортується. Ця фотосистма складається з горизонтального
штативу Beike Q999H з двома LED-лампами Yongnuo YN-300 Air змонтованими на 11” тримачах
Magic Arm. Камеру Canon EOS 800D було обрано завдяки присутності повністю обертового дисплею,
сучасній системі фокусування, підтримці формату RAW, а також низькій ціні на ринку. Об’єктив
Tokina AT-X M35 PRO DX AF 35 mm f/2.8 Macro було обрано завдяки винятковій чіткості на всій
площині зображення, низькому рівню аберацій та оптичної дисторсії, високій світлочутливості, а
також швидкому автофокусу.
Ми також протестували лайт-бокс для оцифрування гербарних зразків. Однак, виявилося, що лайт-
бокс незручний для оцифрування гербарію з кількох причин. Зокрема, він має великі розміри,
обмежений доступ до робочої поверхні, а також вимагає використання масивної несучої конструкції,
яка повинна утримувати камеру високо над центром лайт-боксу. Загалом, використання лайт-боксу
сильно сповільнює процес оцифрування. Ми не знайшли жодних переваг використання лайт-боксу,
і тому відмовилися від його застосування. Ми сподіваємося, що наш досвід буде корисним для інших
кураторів, які прагнуть оцифрувати їхні колекції, але мають обмежений бюджет.
Ключові слова: гербарій, оцифрування, малі колекції, побудова фотосистеми
digitization of the LWS collection. We also
thank Heimo Rainer for consultation, support,
and kindly gifted Color Checker.
References
Baker, B. (2020). Biodiversity collections, data, and
Covid. BioScience, 70(10), 841–847. https://doi.
org/10.1093/biosci/biaa093
Bridson, D., & Forman, L. (2013). Herbarium
handbook. 3rd edition. Kew Royal Botanic Gardens.
Cantrill, D. J. (2018). The Australasian virtual
herbarium: tracking data usage and benefits for
biological collections. Applications In Plant Sciences,
6(2), Article e1026. https://doi.org/10.1002/
aps3.1026
Holovachov, O., Zatushevsky A., & Shydlovsky, I.
(2014). Whole-drawer imaging of entomological
collections: benefits, limitations and alternative
applications. Journal of Conservation and Museum
Studies, 12(1), 9. https://doi.org/10.5334/
jcms.1021218
Novikov, A. (2019, November 27–29). Digitization
of natural collections – the way to immortality.
In Proceedings of the 14th International Young
Scientists’ Conference “Biology: From a Molecule Up
to the Biosphere” (pp. 12–14). Kharkiv. https://doi.
org/10.5281/zenodo.3594474
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
https://doi.org/10.1093/biosci/biaa093
https://doi.org/10.1093/biosci/biaa093
https://doi.org/10.1002/aps3.1026
https://doi.org/10.1002/aps3.1026
https://doi.org/10.5334/jcms.1021218
https://doi.org/10.5334/jcms.1021218
https://doi.org/10.5281/zenodo.3594474
https://doi.org/10.5281/zenodo.3594474
https://doi.org/10.3897/phytokeys.118.29434
https://doi.org/10.3897/phytokeys.118.29434
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| spelling | oai:ojs2.plantintroduction.org:article-15992023-08-26T20:39:08Z Simple and cheap photosystem for herbarium digitization Проста й недорога фотосистема для оцифрування гербарію Novikov, Andriy Sup-Novikova, Mariia The digitization of the natural history collections is a crucial task of today. It allows not only sharing the data but also virtually preserving the specimens. This is especially important for small collections that suffer from limited financial support and can be easily lost. Here we share our experience of the building of cheap and simple photosystem that can be used for routine digitization of local herbaria with low or without incomes. This photosystem is modular and based on the regular components that can be easily purchased and/or updated. It is compact and can be conveniently assembled and disassembled, and transported. This photosystem consists of horizontal tripod Beike Q999H with two led lamps Yongnuo YN-300 Air mounted on the 11” Magic Arm handles. The camera Canon EOS 800D was chosen due to presence of fully rotated display, the high resolution, modern focusing system, RAW format support, and low price on the market. The lens Tokina AT-X M35 PRO DX AF 35 mm f/2.8 Macro was chosen due to extreme sharpness along the whole capturing field, low aberrations and optical distortion, high light sensitivity, and fast autofocus. We also tested light box as an option for herbarium specimens’ digitization. However, we found that light box is inconvenient for herbarium digitization dues several reasons, among which its massive sizes, limited access to working space, and necessity of application of huge mounting system that should hold the camera far higher over the center of light box. In general, work with light box significantly decelerated the digitization process. We did not find any advantaged in use of the light box and therefore it was rejected. We hope that our experience will be useful for other curators wanting to digitize their collections and having limited budget. Оцифрування природничих колекцій на сьогодні постає надзвичайно важливим питанням, яке дозволяє не лише поширювати отримані дані, але й віртуально зберігати зразки. Це особливо важливо для малих колекцій, які регулярно потерпають від недофінансування і можуть бути легко втрачені. В цій публікації ми ділимося досвідом побудови дешевої і простої фотосистеми, що може використовуватися для рутинного оцифрування локальних гербаріїв, які мають обмежений бюджет або й опинилися без фінансової підтримки взагалі. Ця фотосистема є модульною і побудована на звичних компонентах, які можна легко придбати та/або вдосконалити. Вона є компактною, зручно складається і розкладається, а також транспортується. Ця фотосистма складається з горизонтального штативу Beike Q999H з двома LED-лампами Yongnuo YN-300 Air змонтованими на 11” тримачах Magic Arm. Камеру Canon EOS 800D було обрано завдяки присутності повністю обертового дисплею, сучасній системі фокусування, підтримці формату RAW, а також низькій ціні на ринку. Об’єктив Tokina AT-X M35 PRO DX AF 35 mm f/2.8 Macro було обрано завдяки винятковій чіткості на всій площині зображення, низькому рівню аберацій та оптичної дисторсії, високій світлочутливості, а також швидкому автофокусу. Ми також протестували лайт-бокс для оцифрування гербарних зразків. Однак, виявилося, що лайт-бокс незручний для оцифрування гербарію з кількох причин. Зокрема, він має великі розміри, обмежений доступ до робочої поверхні, а також вимагає використання масивної несучої конструкції, яка повинна утримувати камеру високо над центром лайт-боксу. Загалом, використання лайт-боксу сильно сповільнює процес оцифрування. Ми не знайшли жодних переваг використання лайт-боксу, і тому відмовилися від його застосування. Ми сподіваємося, що наш досвід буде корисним для інших кураторів, які прагнуть оцифрувати їхні колекції, але мають обмежений бюджет. M.M. Gryshko National Botanical Garden of the NAS of Ukraine 2021-12-06 Article Article application/pdf https://www.plantintroduction.org/index.php/pi/article/view/1599 10.46341/PI2021015 Plant Introduction; No 91/92 (2021); 50-53 Інтродукція Рослин; № 91/92 (2021); 50-53 2663-290X 1605-6574 10.46341/PI91-92 en https://www.plantintroduction.org/index.php/pi/article/view/1599/1520 Copyright (c) 2021 Andriy Novikov, Mariia Sup-Novikova http://creativecommons.org/licenses/by/4.0 |
| spellingShingle | Novikov, Andriy Sup-Novikova, Mariia Проста й недорога фотосистема для оцифрування гербарію |
| title | Проста й недорога фотосистема для оцифрування гербарію |
| title_alt | Simple and cheap photosystem for herbarium digitization |
| title_full | Проста й недорога фотосистема для оцифрування гербарію |
| title_fullStr | Проста й недорога фотосистема для оцифрування гербарію |
| title_full_unstemmed | Проста й недорога фотосистема для оцифрування гербарію |
| title_short | Проста й недорога фотосистема для оцифрування гербарію |
| title_sort | проста й недорога фотосистема для оцифрування гербарію |
| url | https://www.plantintroduction.org/index.php/pi/article/view/1599 |
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