Micrograph Extension For Quarto

Quarto shortcode extension to display micrographs in revealjs presentations

Features not implemented but on the wish list

In descending order of priority:

• Some sort of PowerPoint export support, even if only linked to HTML or static image.
• Add scalebar option.
• Support for 16-bit raw tif.
• Panel to change LUT configuration instead of default RGB:
  • 🔵🟢🟣 blue, green, magenta BGM.
  • 🔵🩵🔴 blue, cyan, red BCR.
  • 🔵🟡🔴 blue, yellow, red BYR.
• Re-arrange channel order.
• Hide control panels and make them appear on a click.
• Change layout and size of individual panels.
• Support for video files.

Installing quarto

Go to this site to install Quarto CLI, VScode recommend as IDE: https://quarto.org/docs/get-started/

Also recommend the VScode Quarto extension: https://quarto.org/docs/tools/vscode.html

Installing the extension for your project

quarto add furthlab/micrograph

This will install the extension under the _extensions subdirectory. If you're using version control, you will want to check in this directory.

Using

The shortcode has the formula:

{{< micrograph >}}

• First argument is path to file (e.g. ./img/GFP.jpg).
• Second argument is name of the blue channel (default DAPI).
• Third argument is name of the green channel (default Phalloidin).
• Fourth argument is name of the red channel (default anti-FLAG).
• Optional arguments are:
  • width = "255" default is 255px.

Full example:

{{< micrograph ./img/GFP.jpg DAPI Phalloidin GFP width="255" >}}

Example

Check our the source code for a minimal example using revealjs for the presentation: example.qmd.

---
title: "Micrograph Example"
author: "John Doe"
format: revealjs
---

## Micrograph result

{{< micrograph ./resources/MAX_240329_PC3_Rab_Anti_FlagTag_647_E300_I300_Phallodin_594_E100_I500_DAPI_E300_I300_1_MMStack_Pos0.ome.jpg DAPI Phalloidin anti-FLAG width="255" >}}

- **Primary antibody:** 1:1000 overnight
- **Secondary antibody:** 1:1000 for 1h