From a241f6f753e2f9c571a63f0e44b4f6c8adced499 Mon Sep 17 00:00:00 2001 From: anouk4 Date: Tue, 4 Nov 2025 11:13:07 +0100 Subject: [PATCH 01/17] add sop-040-nl empty template --- .../.zenodo.json | 31 ++++ .../01_afhankelijkheden.Rmd | 49 ++++++ .../02_onderwerp.Rmd | 15 ++ .../03_definities_afkortingen.Rmd | 7 + .../04_competenties.Rmd | 8 + .../05_proces.Rmd | 8 + .../06_werkwijze.Rmd | 9 + .../07_veiligheid.Rmd | 7 + .../08_referenties.Rmd | 5 + .../09_appendices.Rmd | 1 + .../10_subprotocols.Rmd | 21 +++ .../LICENSE.md | 159 ++++++++++++++++++ .../sop_040_nl_imagej_ongewervelden/NEWS.md | 22 +++ .../_bookdown.yml | 30 ++++ .../_output.yml | 18 ++ .../sop_040_nl_imagej_ongewervelden/index.Rmd | 97 +++++++++++ .../organisation.yml | 13 ++ .../referenties.yaml | 0 18 files changed, 500 insertions(+) create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/.zenodo.json create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/01_afhankelijkheden.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/09_appendices.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/10_subprotocols.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/LICENSE.md create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/_bookdown.yml create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/_output.yml create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/organisation.yml create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/referenties.yaml diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/.zenodo.json b/source/sop/sop_040_nl_imagej_ongewervelden/.zenodo.json new file mode 100644 index 00000000..f3e6bce2 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/.zenodo.json @@ -0,0 +1,31 @@ +{ + "description": "", + "title": "Abundantie- en oppervlaktebepaling van groepsfoto’s met ongewervelden in ImageJ.", + "upload_type": "publication", + "access_right": "open", + "license": "CC-BY-4.0", + "keywords": [ + "imagej; beeldverwerking" + ], + "publisher": "Instituut voor Natuur- en Bosonderzoek (INBO)", + "contributors": [ + { + "name": "Ollevier, Anouk", + "affiliation": "Instituut voor Natuur- en Bosonderzoek (INBO)", + "orcid": "0000-0003-2758-4723", + "type": "contactperson" + } + ], + "creators": [ + { + "name": "Ollevier, Anouk", + "affiliation": "Instituut voor Natuur- en Bosonderzoek (INBO)", + "orcid": "0000-0003-2758-4723" + } + ], + "communities": [ + { + "identifier": "inbo" + } + ] +} diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/01_afhankelijkheden.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/01_afhankelijkheden.Rmd new file mode 100644 index 00000000..478ac228 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/01_afhankelijkheden.Rmd @@ -0,0 +1,49 @@ +# Afhankelijkheden + +```{=html} + +``` +```{r dependencies} +empty_table <- tibble( + protocol_code = character(), + version_number = character(), + params = character(), + appendix = logical() +) %>% + add_row() %>% + rename( + `Protocolcode` = protocol_code, + `Versienummer` = version_number, + `Opgenomen als subprotocol` = appendix + ) %>% + pander::pander(split.tables = Inf) + +if (exists("params")) { + if (!is.null(params$dependencies)) { + transpose(params$dependencies) %>% + as_tibble() %>% + mutate(protocol_code = as.character(protocol_code), + version_number = as.character(version_number), + params = as.character(params), + version_number = ifelse(params == "NA", + paste0("[", version_number, "](../", + version_number, "/", "index.html)"), + version_number), + appendix = as.logical(appendix)) %>% + rename( + `Protocolcode` = protocol_code, + `Versienummer` = version_number, + `Opgenomen als subprotocol` = appendix + ) %>% + pander::pander(split.tables = Inf) + } else { + empty_table + } +} else { + empty_table +} +rm(empty_table) +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd new file mode 100644 index 00000000..11466925 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd @@ -0,0 +1,15 @@ +# Onderwerp + +```{=html} + +``` + + + + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd new file mode 100644 index 00000000..6d11a357 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd @@ -0,0 +1,7 @@ +# Definities en afkortingen + +```{=html} + +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd new file mode 100644 index 00000000..83f0c166 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd @@ -0,0 +1,8 @@ +# Vereiste competenties en opleidingen + +```{=html} + +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd new file mode 100644 index 00000000..2994a1d9 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd @@ -0,0 +1,8 @@ +# Proces + +```{=html} + +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd new file mode 100644 index 00000000..c1424f33 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd @@ -0,0 +1,9 @@ +# Werkwijze + +```{=html} + +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd new file mode 100644 index 00000000..33cd546f --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd @@ -0,0 +1,7 @@ +# Veiligheid + +```{=html} + +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd new file mode 100644 index 00000000..317a4928 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd @@ -0,0 +1,5 @@ +# Referenties {.unnumbered} + +::: {#refs} +\item +::: diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/09_appendices.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/09_appendices.Rmd new file mode 100644 index 00000000..61e6766a --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/09_appendices.Rmd @@ -0,0 +1 @@ +# (APPENDIX) Bijlagen {.unnumbered} diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/10_subprotocols.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/10_subprotocols.Rmd new file mode 100644 index 00000000..82f367e3 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/10_subprotocols.Rmd @@ -0,0 +1,21 @@ +```{r, results="asis"} +if (exists("params")) { + if (!is.null(params$dependencies)) { + mdfiles <- paste0(map_chr(params$dependencies, "protocol_code"), + "-", + map_chr(params$dependencies, "version_number"), + ".md") + child_docs <- file.path(map_chr(params$dependencies, "version_number"), + mdfiles) + + child_docs <- child_docs[map_lgl(params$dependencies, "appendix")] + + if (length(child_docs) > 0) { + res <- map(child_docs, knit_child, quiet = TRUE) + cat( + c("# (PART) Subprotocols {.unnumbered}", "", unlist(res)), sep = "\n" + ) + } + } +} +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/LICENSE.md b/source/sop/sop_040_nl_imagej_ongewervelden/LICENSE.md new file mode 100644 index 00000000..bed44e07 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/LICENSE.md @@ -0,0 +1,159 @@ +# Creative Commons Attribution 4.0 International + +Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. 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If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions. + +c. No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor. + +d. Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority. + +``` +Creative Commons is not a party to its public licenses. Notwithstanding, Creative Commons may elect to apply one of its public licenses to material it publishes and in those instances will be considered the “Licensor.” Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at [creativecommons.org/policies](http://creativecommons.org/policies), Creative Commons does not authorize the use of the trademark “Creative Commons” or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses. + +Creative Commons may be contacted at [creativecommons.org](http://creativecommons.org/). +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md b/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md new file mode 100644 index 00000000..59564693 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md @@ -0,0 +1,22 @@ +# Wijzigingen t.o.v. vorige versies + +## [2025.03](../2025.03/index.html) + +- ... + +```{=html} + +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/_bookdown.yml b/source/sop/sop_040_nl_imagej_ongewervelden/_bookdown.yml new file mode 100644 index 00000000..784772d7 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/_bookdown.yml @@ -0,0 +1,30 @@ +book_filename: sop_040_nl_imagej_ongewervelden.Rmd +delete_merged_file: true +rmd_files: +- index.Rmd +- NEWS.md +- 01_afhankelijkheden.Rmd +- 02_onderwerp.Rmd +- 03_definities_afkortingen.Rmd +- 04_competenties.Rmd +- 05_proces.Rmd +- 06_werkwijze.Rmd +- 07_veiligheid.Rmd +- 08_referenties.Rmd +- 09_appendices.Rmd +- 10_subprotocols.Rmd +output_dir: ../../../../protocoldocs/docs/sop/sop_040_nl_imagej_ongewervelden +language: + label: + fig: 'Figuur ' + tab: 'Tabel ' + eq: 'Vergelijking ' + thm: 'Theorema ' + lem: 'Lemma ' + def: 'Definitie ' + cor: 'Bijgevolg ' + prp: 'Propositie ' + ex: 'Voorbeeld ' + proof: 'Bewijs. ' + remark: 'Opmerking. ' + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/_output.yml b/source/sop/sop_040_nl_imagej_ongewervelden/_output.yml new file mode 100644 index 00000000..71dc0414 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/_output.yml @@ -0,0 +1,18 @@ + +bookdown::gitbook: + split_by: none + split_bib: no + template: !expr protocolhelper:::protocol_css() + css: css/inbo_rapport.css + config: + toc: + before: + - + - + after: + -
    • +bookdown::pdf_book: + keep_tex: no + pandoc_args: --top-level-division=chapter + template: !expr protocolhelper:::protocol_tex() + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd new file mode 100644 index 00000000..97720f2a --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd @@ -0,0 +1,97 @@ +--- +title: "Abundantie- en oppervlaktebepaling van groepsfoto’s met ongewervelden in ImageJ" +author: + - name: + given: "Anouk" + family: "Ollevier" + email: "anouk.ollevier@inbo.be" + orcid: "0000-0003-2758-4723" + affiliation: "Instituut voor Natuur- en Bosonderzoek (INBO)" + corresponding: true +reviewer: + - name: + given: "Jan" + family: "Van Uytvanck" + email: "jan.vanuytvanck@inbo.be" + orcid: "0000-0002-1946-7917" + affiliation: "Instituut voor Natuur- en Bosonderzoek (INBO)" +file_manager: + - name: + given: "Jan" + family: "Van Uytvanck" + email: "jan.vanuytvanck@inbo.be" + orcid: "0000-0002-1946-7917" + affiliation: "Instituut voor Natuur- en Bosonderzoek (INBO)" +keywords: "imagej; beeldverwerking" +language: nl +date: "`r Sys.Date()`" +protocol_code: sop-040-nl +version_number: "2025.03" +template_name: sop +community: "inbo" +publisher: Instituut voor Natuur- en Bosonderzoek (INBO) +site: bookdown::bookdown_site +bibliography: referenties.yaml +link-citations: TRUE +csl: https://raw.githubusercontent.com/citation-style-language/styles/master/research-institute-for-nature-and-forest.csl +--- + +```{=html} + +``` +```{r setup, include=FALSE} +library(knitr) +opts_chunk$set( + echo = FALSE, + eval = TRUE, + dpi = 300, + fig.width = 150 / 25.4, + fig.height = 100 / 25.4, + out.width = "100%", + warning = FALSE, + error = TRUE, + message = FALSE +) +library(dplyr) +library(purrr) +library(protocolhelper) +library(pander) +panderOptions("table.alignment.default", "left") +metadata <- rmarkdown::metadata +path_to_protocol <- get_path_to_protocol(metadata$protocol_code) +type <- get_protocol_type(metadata$protocol_code, auto_identifier = TRUE) +``` + +# Metadata {.unnumbered} + +```{r metadata-table} +revs <- map_chr( + metadata[["reviewer"]], + \(x) x$name |> paste(collapse = " ") +) +fms <- map_chr( + metadata[["file_manager"]], + \(x) x$name |> paste(collapse = " ") +) +tibble( + reviewers = revs, + documentbeheerder = fms, + protocolcode = metadata[["protocol_code"]], + versienummer = metadata[["version_number"]], + taal = metadata[["language"]] +) %>% + pander::pander(split.tables = Inf) +rm(revs, fms) +``` + +```{r results="asis"} +sprintf("Controleer [deze tabel](../%s.html){target=\"_blank\"} om te zien of een meer recente versie beschikbaar is.", type) |> cat() # nolint +``` diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/organisation.yml b/source/sop/sop_040_nl_imagej_ongewervelden/organisation.yml new file mode 100644 index 00000000..cf69e432 --- /dev/null +++ b/source/sop/sop_040_nl_imagej_ongewervelden/organisation.yml @@ -0,0 +1,13 @@ +community: inbo +email: info@inbo.be +github: inbo +funder: Research Institute for Nature and Forest (INBO) +rightsholder: Research Institute for Nature and Forest (INBO) +organisation: + inbo.be: + affiliation: + - Research Institute for Nature and Forest (INBO) + - Instituut voor Natuur- en Bosonderzoek (INBO) + - Institut de Recherche sur la Nature et les Forêts (INBO) + - Institut für Natur- und Waldforschung (INBO) + orcid: yes diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/referenties.yaml b/source/sop/sop_040_nl_imagej_ongewervelden/referenties.yaml new file mode 100644 index 00000000..e69de29b From 7183ee39f826c1e6ae61ab8579422a5c6d133956 Mon Sep 17 00:00:00 2001 From: anouk4 Date: Tue, 4 Nov 2025 15:28:55 +0100 Subject: [PATCH 02/17] Ingevuld protocol --- .../02_onderwerp.Rmd | 4 + .../03_definities_afkortingen.Rmd | 3 + .../04_competenties.Rmd | 3 + .../05_proces.Rmd | 3 + .../06_werkwijze.Rmd | 88 ++++++++++++++++++ .../07_veiligheid.Rmd | 3 + .../08_referenties.Rmd | 12 ++- .../sop_040_nl_imagej_ongewervelden/index.Rmd | 17 +++- .../media/Afbeelding1.png | Bin 0 -> 38793 bytes 9 files changed, 127 insertions(+), 6 deletions(-) create mode 100644 source/sop/sop_040_nl_imagej_ongewervelden/media/Afbeelding1.png diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd index 11466925..b0e044cc 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd @@ -12,4 +12,8 @@ Toepassingsgebied: bespreek hier onder welke condities het protocol kan gebruikt +Binnen het Procesbeheerproject [1] worden in elk subplot twee keer per jaar stalen van ongewervelden verzameld: één keer in mei-juni en één keer in augustus-september. +In het labo worden de ongewervelden via triage uit het strooisel gescheiden en vervolgens per taxonomische groep gesorteerd. +Met dit materiaal worden (a) groepsfoto’s gemaakt, waarop per taxonomische groep het aantal individuen en het oppervlak wordt bepaald in ImageJ (zie hiervoor deze SOP), en (b) de exemplaren gedetermineerd en ingevoerd in waarnemingen.be. + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd index 6d11a357..b43c7c3c 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/03_definities_afkortingen.Rmd @@ -5,3 +5,6 @@ Definities van begrippen en afkortingen die noodzakelijk zijn om dit document te begrijpen en het protocol op een gepaste manier te kunnen uitvoeren. --> ``` + +N.v.t. + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd index 83f0c166..d9b4ce3f 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/04_competenties.Rmd @@ -6,3 +6,6 @@ Omschrijving van de basiskennis en vaardigheden, die de gebruiker van het protoc Eventueel kan er verwezen worden naar bepaalde opleidingen. --> ``` + +N.v.t. + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd index 2994a1d9..bd9b1a9b 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/05_proces.Rmd @@ -6,3 +6,6 @@ gebruik bijvoorbeeld `draw.io` en exporteer als png of maak het schema met een R package zoals `visNetwork` --> ``` + +N.v.t. + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd index c1424f33..496cb1c0 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd @@ -1,3 +1,9 @@ +--- +editor_options: + markdown: + wrap: 72 +--- + # Werkwijze ```{=html} @@ -7,3 +13,85 @@ Deze stappen staan schematisch weergegeven in het processchema. Subtitels gebruiken om elke stap te omschrijven. --> ``` + +## 1. Openen van de foto + +Open ImageJ [2] + +Laad de groepsfoto in via File \> Open + +De groepsfoto’s vbevinden zich in de map: G:\Gedeelde +drives\Procesbeheer\PB11_Plotbemonstering\PB\_Plot_Invertebraten\FOTO\_SubPlot_Invertebraten\Groepsfoto + +## 2. Schaal instellen + +Gebruik de Straight line tool en trek een lijn tussen de twee aangeduide +referentiepunten. In het labo werden de punten werden zo geplaatst dat +ze op een afstand van 50 of 150 mm van elkaar liggen. Als de punten in +een vierkant liggen, zijn beide zijden 150 mm lang. Als ze een balk +vormen, dan is de korte zijde 50 mm en de lange zijde 150 mm. + +Klik vervolgens op Analyze \> Set Scale. De waarde in pixels verschijnt +automatisch. Vul bij Known distance 5 of 15 in, afhankelijk van de +werkelijke afstand, en noteer bij Unit of length “cm”. + +Klik op OK. + +## 3. Threshold instellen + +Klik op Image \> Adjust \> Color Threshold. + +Pas alleen de twee waarden onder Brightness aan: zet de eerste waarde op +0 en kies voor de tweede een waarde tussen 160 en 220. De bedoeling is +dat de organismen duidelijk rood gemarkeerd zijn, zonder dat de +achtergrond te sterk meekleurt. Een paar rode puntjes in de achtergrond +zijn geen probleem, want die kunnen later worden uitgefilterd. + +## 4. Analyse per taxonomische groep Groepeer en selecteer + +de organismen van één bepaalde taxonomische groep via de polygon tool. +Trek een polygon rondom de groep. + +Klik op Analyze \> Analyze particles + +Om ervoor te zorgen dat de kleine rode spikkels op de achtergrond niet +worden mee geanalyseerd stel je Size (cm\^2) in op ‘0.015-Infinity’. Dit +zorgt ervoor dat objecten kleiner dan 0.015 cm² er worden uit gefilterd. + +Kies bij Show voor Overlay Masks, zodat de geselecteerde organismen na +de analyse zichtbaar en genummerd zijn. + +Klik op OK.\ + +```{r} +knitr::include_graphics("media/Afbeelding1.png") +``` + +Via Analyze Particles worden de objecten – hier dus de organismen – +automatisch geteld en gemeten (o.a. oppervlakte). De resultaten +verschijnen in twee vensters: Results, waarin de metingen per +individueel object binnen de polygon worden weergegeven, en Summary, dat +een samenvatting toont van alle metingen voor de geselecteerde groep. + +## 5. Opslaan van resultaten + +Sla zowel het bestand Summary als Results op. Gebruik daarbij een vaste +naamgeving: + +*foto-analyse-typeoutput-subplotcode-diergroep-datum(YYYY-MM-DD)* + +*Bijvoorbeeld: foto-analyse-summary-dwhp-03c-kevers-2022-06-01* + +| Onderdeel | Omschrijving | Omschrijving | +|:---------------------|:-------------------------|:-----------------------| +| foto-analyse | Vast voorvoegsel, zodat alle bestanden van dezelfde analyse makkelijk terug te vinden zijn. | foto-analyse | +| typeoutput | Geeft aan welk type bestand het is: summary of results. | summary | +| subplotcode | De code die verwijst naar de subplot. | dwhp-03c | +| diergroep | De onderzochte diergroep. | kevers, wantsen, spinnen, ... | +| datum (YYYY-MM-DD) | De datum van staalname (dus niet de datum van de analyse in ImageJ). | 2022-06-01 | + +## 6. Herhalen + +Voer stap 4 en 5 opnieuw uit voor elke taxonomische groep die aanwezig +is op de groepsfoto. Zorg ervoor dat alle resultaten op dezelfde manier +benoemd en opgeslagen worden. diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd index 33cd546f..f83b90ed 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/07_veiligheid.Rmd @@ -5,3 +5,6 @@ Alle aandachtspunten in verband met veilig werken. --> ``` + +N.v.t. + diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd index 317a4928..d2af6d5d 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd @@ -1,5 +1,15 @@ # Referenties {.unnumbered} ::: {#refs} -\item +[1] Instituut voor Natuur- en Bosonderzoek. +(z.d.). +Doel. +Procesbeheer INBO. + + +[2] Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. +(2012). +NIH Image to ImageJ: 25 years of image analysis. +Nature Methods, 9(7), 671–675. + ::: diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd index 97720f2a..0c5f646f 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd @@ -15,18 +15,24 @@ reviewer: email: "jan.vanuytvanck@inbo.be" orcid: "0000-0002-1946-7917" affiliation: "Instituut voor Natuur- en Bosonderzoek (INBO)" + - name: + given: "Timon" + family: "Boumon" + email: "timon.boumon@inbo.be" + orcid: "0009-0000-5136-9447" + affiliation: "Instituut voor Natuur- en Bosonderzoek (INBO)" file_manager: - name: - given: "Jan" - family: "Van Uytvanck" - email: "jan.vanuytvanck@inbo.be" - orcid: "0000-0002-1946-7917" + given: "Anouk" + family: "Ollevier" + email: "anouk.ollevier@inbo.be" + orcid: "0000-0003-2758-4723" affiliation: "Instituut voor Natuur- en Bosonderzoek (INBO)" keywords: "imagej; beeldverwerking" language: nl date: "`r Sys.Date()`" protocol_code: sop-040-nl -version_number: "2025.03" +version_number: "2025.01" template_name: sop community: "inbo" publisher: Instituut voor Natuur- en Bosonderzoek (INBO) @@ -47,6 +53,7 @@ Niet alle onderdelen zijn altijd van toepassing. Laat in die gevallen de titels staan en vermeld expliciet "niet van toepassing". --> ``` + ```{r setup, include=FALSE} library(knitr) opts_chunk$set( diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/media/Afbeelding1.png b/source/sop/sop_040_nl_imagej_ongewervelden/media/Afbeelding1.png new file mode 100644 index 0000000000000000000000000000000000000000..e197672e0c2f07c93468dce35a2c84e6f3d3b23a GIT binary patch literal 38793 zcmbT7Wl$W^*XD5zPO!lpg1b8dgA?4{-5r7icXtmEB)D5}cXxMp4eb2icR%db)>dup zhpFzKJ3Ui%`_4V*{Lb@4C@DyxAQ2!zKtP~?q$R$Ck4F#?kY5qtz-NG!+feWU(&f99 z7{s4R!V~ZXjD@JYCJT{(IaC~k00%ZQ&@AC5PoyN z+MQU^H|r~j@$~b5hlC9f={b5RfJrWB^dqyhhNzwrzCYNBE7^T`MVO-L60}{e33NMK zMDg?bF*+)P!=TA>f1v1S>I9{qMjR~gIKPw{%_C%YZcJHT4OLd>ff;TLE85k76>%}!>&2ImH)6Hdn{u~;h2@MY? zP=s|oAjZ-v$U_H^{wTEOA@t+mn6LHoVb$SsAgyQ)t9SM8s-V@hMy(47fMsgNZQlqS zI{*p>@u+E_pb7fI2eh0)TI=QcetIhT*?Yed`u2K1bWeAsy%Bp7YuNIgfUb}2K8L;m z&cagp$k(=B;io##Tu2Mv*sQBIA-(x$ ztEmkLf4ngNX@Arnj3WtHwutS=7(m><@wBwHHs6cI+_i+Io3@ 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zcb8>zp>ur(3-#FMzgUSWW9jZk=5i{YS(&v`Z(J&PA-O~nCbHtk(N{J_5jfvSfU(-z~aPB-`t3?&^C6^e;*r?J$fP3#2J#0w`spq+@!+b&60loQ^Gdf=`JAy z_ss*_XjIjNXZ`^z2SxMTxqf9Aan_N0HCX)n5PwKwO~Nl8=p#+Jy65Pxw%B@J;K$$Hq9!PK6RI1yUx^-0#%7H6 z-T^s44sT~CCJ-$6ZJNR%>S#!|J*#capM4Z&$oX5r7}My2RX;h_cA+*>&LW__IEs+uBgHnTK4& z5H^s0r>d;^rOdQ4-7&TwH-vlr=oB>9jVLZA)%lFNFbVz^vaQy-+bA z&NFfG>>-!;?9ec=>6D>(k_KVa(D-#xRuqmzR=c^tT&KjvkvjlHj=82r!Zv+5iz*eV zCL|>>iIJ+tO|xAZIZp+rzOUA{Y!q5fK1wwnSNFmrgWzAY;mnzbZTsIi|MwdPNIUa1pq z5k^Z$X88{SK?T-VSkwIl(l9|fEwu*}v&{$_O~)e;h%r1KNI@3s@uQQaes;trXenT^ zVP?h0@aa=^E`Y4}p}#OfEhI#4cedW;*SBgrR|__oF@HE9#$FtvqeIydbcg|CPrM2q z&Cky>%fkd)e}uZbPd@CHOloPj`Iz;6;!3giK9LzOAu#WM>kQkco$$ZjZr8V^s;267YCR!nKvL z*_rR(KjhcT9hZCdNI#21A&^k3zb%bqJRs(uQgCt6TJPl4T67I_5%gF?vniCyF1twV z@_i*iPr<&s*X_po?@Wn+auRgfF!cE|gM=tJu0S}olIMS$s4={~BD6qO;Q#KaHt-~$ Wuj2mzK^J7V2%C;3RHIJKKIXrXFBmug literal 0 HcmV?d00001 From 99322cedcd4fd503c14ea175a33b4f7f18f3e60f Mon Sep 17 00:00:00 2001 From: anouk4 Date: Tue, 4 Nov 2025 15:29:25 +0100 Subject: [PATCH 03/17] Ingevuld protocol --- .../02_onderwerp.Rmd | 1 - .../06_werkwijze.Rmd | 100 +++++++++--------- .../08_referenties.Rmd | 2 - 3 files changed, 48 insertions(+), 55 deletions(-) diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd index b0e044cc..55f8dd29 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/02_onderwerp.Rmd @@ -16,4 +16,3 @@ Binnen het Procesbeheerproject [1] worden in elk subplot twee keer per jaar stal In het labo worden de ongewervelden via triage uit het strooisel gescheiden en vervolgens per taxonomische groep gesorteerd. Met dit materiaal worden (a) groepsfoto’s gemaakt, waarop per taxonomische groep het aantal individuen en het oppervlak wordt bepaald in ImageJ (zie hiervoor deze SOP), en (b) de exemplaren gedetermineerd en ingevoerd in waarnemingen.be. - diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd index 496cb1c0..e5a68e07 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/06_werkwijze.Rmd @@ -1,9 +1,3 @@ ---- -editor_options: - markdown: - wrap: 72 ---- - # Werkwijze ```{=html} @@ -14,84 +8,86 @@ Subtitels gebruiken om elke stap te omschrijven. --> ``` -## 1. Openen van de foto +## Openen van de foto Open ImageJ [2] Laad de groepsfoto in via File \> Open -De groepsfoto’s vbevinden zich in de map: G:\Gedeelde -drives\Procesbeheer\PB11_Plotbemonstering\PB\_Plot_Invertebraten\FOTO\_SubPlot_Invertebraten\Groepsfoto +De groepsfoto’s bevinden zich in de map: `G:\Gedeelde drives\Procesbeheer\PB11\_Plotbemonstering\PB\_Plot_Invertebraten\FOTO\_SubPlot_Invertebraten\Groepsfoto` -## 2. Schaal instellen +## Schaal instellen -Gebruik de Straight line tool en trek een lijn tussen de twee aangeduide -referentiepunten. In het labo werden de punten werden zo geplaatst dat -ze op een afstand van 50 of 150 mm van elkaar liggen. Als de punten in -een vierkant liggen, zijn beide zijden 150 mm lang. Als ze een balk -vormen, dan is de korte zijde 50 mm en de lange zijde 150 mm. +Gebruik de Straight line tool en trek een lijn tussen de twee aangeduide referentiepunten. +In het labo werden de punten werden zo geplaatst dat ze op een afstand van 50 of 150 mm van elkaar liggen. +Als de punten in een vierkant liggen, zijn beide zijden 150 mm lang. +Als ze een balk vormen, dan is de korte zijde 50 mm en de lange zijde 150 mm. -Klik vervolgens op Analyze \> Set Scale. De waarde in pixels verschijnt -automatisch. Vul bij Known distance 5 of 15 in, afhankelijk van de -werkelijke afstand, en noteer bij Unit of length “cm”. +Klik vervolgens op Analyze \> Set Scale. +De waarde in pixels verschijnt automatisch. +Vul bij Known distance 5 of 15 in, afhankelijk van de werkelijke afstand, en noteer bij Unit of length “cm”. Klik op OK. -## 3. Threshold instellen +## Threshold instellen Klik op Image \> Adjust \> Color Threshold. -Pas alleen de twee waarden onder Brightness aan: zet de eerste waarde op -0 en kies voor de tweede een waarde tussen 160 en 220. De bedoeling is -dat de organismen duidelijk rood gemarkeerd zijn, zonder dat de -achtergrond te sterk meekleurt. Een paar rode puntjes in de achtergrond -zijn geen probleem, want die kunnen later worden uitgefilterd. +Pas alleen de twee waarden onder Brightness aan: zet de eerste waarde op 0 en kies voor de tweede een waarde tussen 160 en 220. +De bedoeling is dat de organismen duidelijk rood gemarkeerd zijn, zonder dat de achtergrond te sterk meekleurt. +Een paar rode puntjes in de achtergrond zijn geen probleem, want die kunnen later worden uitgefilterd. -## 4. Analyse per taxonomische groep Groepeer en selecteer +## Analyse per taxonomische groep -de organismen van één bepaalde taxonomische groep via de polygon tool. +Groepeer en selecteer de organismen van één bepaalde taxonomische groep via de polygon tool. Trek een polygon rondom de groep. Klik op Analyze \> Analyze particles -Om ervoor te zorgen dat de kleine rode spikkels op de achtergrond niet -worden mee geanalyseerd stel je Size (cm\^2) in op ‘0.015-Infinity’. Dit -zorgt ervoor dat objecten kleiner dan 0.015 cm² er worden uit gefilterd. +Om ervoor te zorgen dat de kleine rode spikkels op de achtergrond niet worden mee geanalyseerd stel je Size (cm\^2) in op ‘0.015-Infinity’. +Dit zorgt ervoor dat objecten kleiner dan 0.015 cm² er worden uit gefilterd. -Kies bij Show voor Overlay Masks, zodat de geselecteerde organismen na -de analyse zichtbaar en genummerd zijn. +Kies bij Show voor Overlay Masks, zodat de geselecteerde organismen na de analyse zichtbaar en genummerd zijn. Klik op OK.\ -```{r} -knitr::include_graphics("media/Afbeelding1.png") +(ref:afbeelding1) Analyze Particles scherm + +```{r afbeelding1, fig.cap="(ref:afbeelding1)", out.width="33%"} +knitr::include_graphics(file.path(path_to_protocol, "media/Afbeelding1.png")) ``` -Via Analyze Particles worden de objecten – hier dus de organismen – -automatisch geteld en gemeten (o.a. oppervlakte). De resultaten -verschijnen in twee vensters: Results, waarin de metingen per -individueel object binnen de polygon worden weergegeven, en Summary, dat -een samenvatting toont van alle metingen voor de geselecteerde groep. +Via Analyze Particles worden de objecten – hier dus de organismen – automatisch geteld en gemeten (o.a. oppervlakte) (zie figuur \@ref(fig:afbeelding1)). +De resultaten verschijnen in twee vensters: Results, waarin de metingen per individueel object binnen de polygon worden weergegeven, en Summary, dat een samenvatting toont van alle metingen voor de geselecteerde groep. -## 5. Opslaan van resultaten +## Opslaan van resultaten -Sla zowel het bestand Summary als Results op. Gebruik daarbij een vaste -naamgeving: +Sla zowel het bestand Summary als Results op. +Gebruik daarbij een vaste naamgeving: *foto-analyse-typeoutput-subplotcode-diergroep-datum(YYYY-MM-DD)* *Bijvoorbeeld: foto-analyse-summary-dwhp-03c-kevers-2022-06-01* -| Onderdeel | Omschrijving | Omschrijving | -|:---------------------|:-------------------------|:-----------------------| -| foto-analyse | Vast voorvoegsel, zodat alle bestanden van dezelfde analyse makkelijk terug te vinden zijn. | foto-analyse | -| typeoutput | Geeft aan welk type bestand het is: summary of results. | summary | -| subplotcode | De code die verwijst naar de subplot. | dwhp-03c | -| diergroep | De onderzochte diergroep. | kevers, wantsen, spinnen, ... | -| datum (YYYY-MM-DD) | De datum van staalname (dus niet de datum van de analyse in ImageJ). | 2022-06-01 | +```{r} +df <- data.frame( + Onderdeel = c("foto-analyse", "typeoutput", "subplotcode", "diergroep", "datum (YYYY-MM-DD)"), + Omschrijving = c( + "Vast voorvoegsel, zodat alle bestanden van dezelfde analyse makkelijk terug te vinden zijn.", + "Geeft aan welk type bestand het is: summary of results.", + "De code die verwijst naar de subplot.", + "De onderzochte diergroep.", + "De datum van staalname (dus niet de datum van de analyse in ImageJ)." + ), + Waarde = c("foto-analyse", "summary", "dwhp-03c", "kevers, wantsen, spinnen, ...", "2022-06-01"), + stringsAsFactors = FALSE +) + +pander(df, caption = add_label("Overzicht naamgeving"), split.tables = Inf) + +``` -## 6. Herhalen +## Herhalen -Voer stap 4 en 5 opnieuw uit voor elke taxonomische groep die aanwezig -is op de groepsfoto. Zorg ervoor dat alle resultaten op dezelfde manier -benoemd en opgeslagen worden. +Voer stap 4 en 5 opnieuw uit voor elke taxonomische groep die aanwezig is op de groepsfoto. +Zorg ervoor dat alle resultaten op dezelfde manier benoemd en opgeslagen worden. diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd b/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd index d2af6d5d..e1f7f0d4 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd +++ b/source/sop/sop_040_nl_imagej_ongewervelden/08_referenties.Rmd @@ -1,6 +1,5 @@ # Referenties {.unnumbered} -::: {#refs} [1] Instituut voor Natuur- en Bosonderzoek. (z.d.). Doel. @@ -12,4 +11,3 @@ Procesbeheer INBO. NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. -::: From 3923e11aa7ca75c8ea8e6f9c965d053442809178 Mon Sep 17 00:00:00 2001 From: anouk4 Date: Tue, 4 Nov 2025 15:35:37 +0100 Subject: [PATCH 04/17] versienummer ongedaan --- source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md | 2 +- source/sop/sop_040_nl_imagej_ongewervelden/index.Rmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md b/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md index 59564693..48fc1f07 100644 --- a/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md +++ b/source/sop/sop_040_nl_imagej_ongewervelden/NEWS.md @@ -2,7 +2,7 @@ ## [2025.03](../2025.03/index.html) -- ... +- Eerste versie van het protocol. ```{=html}