Add poster content for 2024 SBI2 conference

CITATION.cff

@@ -14,6 +14,9 @@ authors:
   - given-names: David
     family-names: Bunten
     orcid: 'https://orcid.org/0000-0001-6041-3665'
+  - given-names: Vincent
+    family-names: Rubinetti
+    orcid: 'https://orcid.org/0000-0002-4655-3773'
   - given-names: Gregory
     family-names: Way
     orcid: 'https://orcid.org/0000-0002-0503-9348'

docs/presentations/2024-09-18-SBI2-Conference/.gitignore

@@ -0,0 +1 @@
+/.quarto/

docs/presentations/2024-09-18-SBI2-Conference/_extensions/quarto-ext/poster/_extension.yml

@@ -0,0 +1,10 @@
+title: Poster (modified)
+author: Carlos Scheidegger, Dave Bunten
+version: 1.0.0
+quarto-required: ">=1.4.415"
+contributes:
+  formats:
+    typst:
+      template-partials:
+        - typst-template.typ
+        - typst-show.typ

docs/presentations/2024-09-18-SBI2-Conference/_extensions/quarto-ext/poster/typst-show.typ

@@ -0,0 +1,74 @@
+// Typst custom formats typically consist of a 'typst-template.typ' (which is
+// the source code for a typst template) and a 'typst-show.typ' which calls the
+// template's function (forwarding Pandoc metadata values as required)
+//
+// This is an example 'typst-show.typ' file (based on the default template
+// that ships with Quarto). It calls the typst function named 'article' which
+// is defined in the 'typst-template.typ' file.
+//
+// If you are creating or packaging a custom typst template you will likely
+// want to replace this file and 'typst-template.typ' entirely. You can find
+// documentation on creating typst templates here and some examples here:
+//   - https://typst.app/docs/tutorial/making-a-template/
+//   - https://github.com/typst/templates
+
+#show: doc => poster(
+  $if(title)$ title: [$title$], $endif$
+  // TODO: use Quarto's normalized metadata.
+  $if(poster-authors)$ authors: [$poster-authors$], $endif$
+  $if(departments)$ departments: [$departments$], $endif$
+  $if(size)$ size: "$size$", $endif$
+
+  // Institution logo.
+  $if(institution-logo)$ univ_logo: "$institution-logo$", $endif$
+
+  // Footer text.
+  // For instance, Name of Conference, Date, Location.
+  // or Course Name, Date, Instructor.
+  $if(footer-text)$ footer_text: [$footer-text$], $endif$
+
+  // Any URL, like a link to the conference website.
+  $if(footer-url)$ footer_url: [$footer-url$], $endif$
+
+  // Emails of the authors.
+  $if(footer-emails)$ footer_email_ids: [$footer-emails$], $endif$
+
+  // Color of the footer.
+  $if(footer-color)$ footer_color: "$footer-color$", $endif$
+
+  // DEFAULTS
+  // ========
+  // For 3-column posters, these are generally good defaults.
+  // Tested on 36in x 24in, 48in x 36in, and 36in x 48in posters.
+  // For 2-column posters, you may need to tweak these values.
+  // See ./examples/example_2_column_18_24.typ for an example.
+
+  // Any keywords or index terms that you want to highlight at the beginning.
+  $if(keywords)$ keywords: ($for(keywords)$"$it$"$sep$, $endfor$), $endif$
+
+  // Number of columns in the poster.
+  $if(num-columns)$ num_columns: $num-columns$, $endif$
+
+  // University logo's scale (in %).
+  $if(univ-logo-scale)$ univ_logo_scale: $univ-logo-scale$, $endif$
+
+  // University logo's column size (in in).
+  $if(univ-logo-column-size)$ univ_logo_column_size: $univ-logo-column-size$, $endif$
+
+  // Title and authors' column size (in in).
+  $if(title-column-size)$ title_column_size: $title-column-size$, $endif$
+
+  // Poster title's font size (in pt).
+  $if(title-font-size)$ title_font_size: $title-font-size$, $endif$
+
+  // Authors' font size (in pt).
+  $if(authors-font-size)$ authors_font_size: $authors-font-size$, $endif$
+
+  // Footer's URL and email font size (in pt).
+  $if(footer-url-font-size)$ footer_url_font_size: $footer-url-font-size$, $endif$
+
+  // Footer's text font size (in pt).
+  $if(footer-text-font-size)$ footer_text_font_size: [$footer-text-font-size$], $endif$
+
+  doc,
+)

docs/presentations/2024-09-18-SBI2-Conference/_extensions/quarto-ext/poster/typst-template.typ

@@ -0,0 +1,173 @@
+#let poster(
+  // set variables for use throughout
+  // note: some are referenced from `.qmd` file
+  size: "'36x24' or '48x36''",
+  title: "Paper Title",
+  authors: "Author Names (separated by commas)",
+  departments: "Department Name",
+  univ_logo: "Logo Path",
+  footer_text: "Footer Text",
+  footer_url: "Footer URL",
+  footer_email_ids: "Email IDs (separated by commas)",
+  footer_color: "Hex Color Code",
+  keywords: (),
+  num_columns: "4",
+  univ_logo_scale: "140",
+  univ_logo_column_size: "15",
+  title_column_size: "25",
+  title_font_size: "48",
+  authors_font_size: "36",
+  footer_url_font_size: "40",
+  footer_text_font_size: "40",
+  body
+) = {
+  // initialize template display formatting
+  set text(font: "Lato", size: 32pt)
+  let sizes = size.split("x")
+  let width = int(sizes.at(0)) * 1in
+  let height = int(sizes.at(1)) * 1in
+  univ_logo_scale = int(univ_logo_scale) * 1%
+  title_font_size = int(title_font_size) * 1pt
+  authors_font_size = int(authors_font_size) * 1pt
+  num_columns = int(num_columns)
+  univ_logo_column_size = int(univ_logo_column_size) * 1in
+  title_column_size = int(title_column_size) * 1in
+  footer_url_font_size = int(footer_url_font_size) * 1pt
+  footer_text_font_size = int(footer_text_font_size) * 1pt
+
+  // create overall page output
+  set page(
+    // total dimensions
+    width: width,
+    height: height,
+    // margin on all sides
+    margin:
+      (top: .8in, left: .8in, right: .8in, bottom: 1.8in),
+    // footer section
+    footer: [
+      #set align(center)
+      #set text(42pt)
+      #block(
+        fill: rgb(footer_color),
+        width: 100%,
+        inset: 20pt,
+        radius: 10pt,
+        // adds text to footer
+        [
+          #text(font: "Lato", size: footer_url_font_size, footer_url)
+          #h(1fr)
+          #text(size: footer_text_font_size, smallcaps(footer_text))
+          #h(1fr)
+          #text(font: "Lato", size: footer_url_font_size, footer_email_ids)
+        ]
+      )
+    ]
+  )
+
+  // set math display properties
+  set math.equation(numbering: "(1)")
+  show math.equation: set block(spacing: 0.65em)
+
+  set enum(indent: 10pt, body-indent: 9pt)
+  set list(indent: 10pt, body-indent: 9pt)
+
+  // set the heading numbering system
+  set heading(numbering: "I.A.1.")
+  show heading: it => locate(loc => {
+    let levels = counter(heading).at(loc)
+    let deepest = if levels != () {
+      levels.last()
+    } else {
+      1
+    }
+
+    // defines how sub-headers display
+    set text(24pt, weight: 400)
+    // sub-header level 1
+    if it.level == 1 [
+      #set text(style: "italic")
+      #v(32pt, weak: true)
+      #if it.numbering != none {
+        numbering("i.", deepest)
+        h(7pt, weak: true)
+      }
+      #it.body
+    // sub-header level 2
+    ] else if it.level == 2 [
+      #v(10pt, weak: true)
+      #set align(left)
+      #set text({ 40pt }, weight: 600, font: "Merriweather", fill: rgb(31, 23, 112))
+      #show: smallcaps
+      #v(50pt, weak: true)
+      #if it.numbering != none {
+        numbering("I.", deepest)
+        h(7pt, weak: true)
+      }
+      #it.body
+      #v(30pt, weak: true)
+      #line(length: 100%, stroke: rgb(200, 200, 200))
+      #v(30pt, weak: true)
+    // all other headers
+    ] else [
+      #set text({ 36pt }, weight: 600, font: "Merriweather", fill: rgb(31, 23, 112))
+      #if it.level == 3 {
+        numbering("☆ 1)", deepest)
+        [ ]
+      }
+      ___#(it.body)___
+      #v(40pt, weak: true)
+    ]
+  })
+
+  // header grid
+  align(left,
+    grid(
+      // rows and cols in the header
+      rows: (auto, auto),
+      columns: (title_column_size, univ_logo_column_size),
+      column-gutter: 5pt,
+      row-gutter: 30pt,
+      // main title
+      text(font: "Merriweather", weight: 1000, size: 48pt, title),
+      grid.cell(
+        image(univ_logo, width: univ_logo_scale),
+        rowspan: 3,
+        align: left,
+      ),
+      // author display
+      text(size: 38pt, authors),
+      // department and notes display
+      text(size: 29pt, emph(departments)),
+    )
+  )
+
+  // spacing between the header and body
+  v(40pt)
+
+  // set main body display
+  show: columns.with(num_columns, gutter: 60pt)
+  // paragraph display properties
+  set par(leading: 10pt,
+    justify: false,
+    first-line-indent: 0em,
+    linebreaks: "optimized"
+  )
+
+  // Configure figures.
+  show figure: it => block({
+    // Display a backdrop rectangle.
+    it.body
+
+    // Display caption.
+    if it.has("caption") {
+      set align(left)
+      v(if it.has("gap") { it.gap } else { 24pt }, weak: true)
+      set text(weight: "bold")
+      it.caption
+    }
+
+  })
+
+  // adds body content to page
+  body
+}

docs/presentations/2024-09-18-SBI2-Conference/abstract.md

@@ -0,0 +1,15 @@
+# SBI2 2024 Abstract Submission - coSMicQC
+
+## Author(s):
+
+Dave Bunten, Jenna Tomkinson, Gregory Way
+
+## Title (under 100 characters):
+
+Single-cell Morphology Quality Control (coSMicQC)
+
+## Abstract (under 500 words):
+
+High-dimensional single-cell morphology data from large-scale microscopy drug screening applications help prioritize effective treatments for patients suffering from various diseases and enable the discovery of new biological mechanisms. Image analysis pipelines to process these single-cell data often introduce errors in the segmentation step, where software improperly segments single cells (for example, capturing undersized or overly large portions of a cell compartment) and incorrectly identifies artifacts like dust or other debris as single cells. These errors lead to erroneous single-cell measurements which need to be removed prior to single-cell analyses to help ensure accurate results. Research scientists often use bespoke approaches to filter single cells or aggregate all single cells into bulk profiles, reducing errors' impact and preventing single-cell analysis. This leads to duplicated effort, human error, and a lack of quality control in single-cell feature data which overall may result in a reduced potential for discoveries or inaccurate outcomes.
+
+We introduce a Python package called coSMicQC (Single cell Morphology Quality Control) to improve single-cell morphology analysis. coSMicQC uses high-content morphology measurements to define default thresholds for removing single cells and enables users to customize quality control parameters. Accessible through both command line interface (CLI) and Python application programming interface (API), coSMicQC seamlessly integrates into diverse analytical workflows, including standalone scripts/workflows to interactive Jupyter Notebooks. Notably, the package creates interactive and exportable visualizations that illustrate outlier distributions. The backbone of this package is a novel data format: the CytoDataFrame. CytoDataFrames facilitate real-time exploration of single-cell images within any pandas environment to seamlessly link single-cell morphology measurements with single-cell images. Leveraging real-world datasets, including Joint Undertaking in Morphological Profiling (CPJUMP1) data, we show how our tool empowers researchers to identify technical outliers within single-cell profile features and improve single-cell analysis.