Francesco Giorlando

Open Scientific Publishing -- how open peer review and publishing can improve science

Mon, 16 Feb 2026 00:00:00 +0000

It’s no secret that there are significant structural problems in the scientific publishing ecosystem, both in publication quality and confidence in the process of publication. There have been many analyses provided by the scientific community and the publishers themselves regarding this crisis.¹ ² ³ ⁴

This post will briefly analyse the current issues and potential solutions before presenting a technical solution designed to improve scientific publishing. We are actively developing an end-to-end, open-source scientific publication and peer-review system, called Reflx. If you’re interested in contributing, then please get in touch!

Using manim and manim-slide for beautiful presentations

Wed, 22 Oct 2025 00:00:00 +0000

Introduction

Making engaging conference presentations is a core part of research. For the recent Models of Consciousness 2025 Conference I tried using the wonderful manim software to create rich web-compatible animations as part of my presentation.

This post describes how to generate similar slides using these tools.

Health AI, a Privacy Minefield

Tue, 26 Sep 2023 00:00:00 +0000

updated 2025-10-14

If the hype is anything to go by, we’re entering a bright future where “Artificial Intelligence” will revolutionize medicine. This post provides some counterpoints to that hype, focusing on three issues:

patient privacy
data sovereignty
professional knowledge and its exploitation

- image (1024x1024) generated using Stable Diffusion v2.0 (Linux, NVIDIA RTX 3090, 24GB)

prompt: creepy humanoid AI doctor looking at medical files, Steps: 20, Sampler: Euler a, CFG scale: 7, Seed: 403319539, Size: 512x512, Model hash: de2f2560, Batch size: 4, Batch pos: 0

Collaborative RMarkdown Hack

Mon, 27 Jul 2020 00:00:00 +0000

Document editing and report creation are key parts of any researcher’s workflow. Thankfully, the tools to edit research documents have improved greatly over the last few years. While I used to write most documents with $ \LaTeX $ , I’d now recommend that researchers use R Markdown.

R Markdown allows the use of R code in a Markdown format and is also easily extended with features. For example, there is the excellent bookdown package which allows easy use of book formatting, bibliographies and cross-references with Markdown.

Cosmo Communicator Review

Sat, 04 Jan 2020 00:00:00 +0000

Introduction

The Cosmo Communicator by Planet Computers is the bastard child of a mobile phone and a mini-laptop. And that’s a good thing. The inquisitive two-year old at home calls it a “puter” and he knows the word for “phone”.

This review will look into what makes this device tick, why I bought one and what sort of uses it lends itself to. I will focus primarily on the user experience.

Inexpensive Router Network with DD-WRT

Sat, 05 Oct 2019 00:00:00 +0000

Introduction

Setting up wireless networking can be a frustrating experience. Available commercial routers vary greatly in their implementation and standards compliance, meaning that compatability between brands of router can be problematic. There are also significant security issues in implementing WiFi netowrks, compounded by the fact that manufacturers rarely update their firmwares and dump support for routers after only a few updates.

Thankfully, there are now some great options for installing open-source software on routers so that it’s easier to have cross-compatibility and maintain up-to-date security patches. The two main open-source software stacks for WiFi routers are: OpenWRT and DD-WRT. In fact, they are related to each other, with OpenWRT providing a lot of code for DD-WRT. They also serve slightly different interests, OpenWRT is focused on providing an open and modular architecture, ideally allowing low-level access to the nuts and bolts of router features, while DD-WRT aims for simplicity of use with a consisten user interface. There are also other open firmwares with narrower scopes, for example Xwrt-Vortex, Tomato, Advanced Tomato and Gargoyle which provide enhanced features for a smaller subset of routers (generally based on the Broadcom chipsets).

OCR with Tesseract

Sat, 05 Oct 2019 00:00:00 +0000

Introduction

Installing Tesseract

Installation instructions for tesseract are available here

Linux:

OS X:

sudo port install imagemagick
sudo port install tesseract
sudo port install tesseract-eng

Use Tesseract

convert PDF to 8-bit TIFF

convert -density 300 -fill white -draw 'rectangle 10,10 20,20' -background white -alpha Off TechnoCommercialLease.pdf -depth 8 file.tiff

tesseract file.tiff output

The artistry of molecules

Sun, 18 Aug 2019 00:00:00 +0000

this post was previously published on my old website, there’ll be a few of those older but useful posts that I’ll be migrating over in the next little while…

Molecules are beautiful things, intricate and infinitely variable. As part of research publications it can be useful to catch them from their best angles. This short post gives some tips on how to present molecules in publications.

Our model for today is Prostaglandin-F2&#945

High Speed SSD Array with ZFS

Fri, 21 Dec 2018 00:00:00 +0000

Scientific computing increasingly involves handling large amounts of raw data. This is particularly the case for neuroimaging. With increases in processing speed outpacing storage speed, disk i/o has become a limiting factor in many computing applications, especially in multi-user systems.

For my consulting work with GreenAnt Networks, I was asked to build a high-speed disk array for scientific computing and virtual machine storage. This is a brief build log and performance test of the outcome.

Open Journal Publishing Systems

Sun, 29 Jul 2018 00:00:00 +0000

Introduction

Scientific publishing is undergoing a transition from corporate-controlled, for-profit publishing to more open models. While “Open-Access”, is part of this, there are a number of considerations important in true “Open Publishing”:

Free access to the public (who pays for most of the research via their taxes!)
Free submission of articles by authors
Open Data - where original data and analysis workflows are made public
Creative Commons - otherwise known as Copyleft, where rights are retained by the author but the content is usable with attribution
Transparency of the review process (with or without anonymity)
Open software, standards and tools used in the publication process

This post will focus on item (6) from above. While the choice of software tools is rarely considered as part of the Open Publishing ecosystem, it is of key importance. The economics of publishing are highly dependent on software. Open-source software enables the creation of open journals. This post will be followed-up with some discussion in the frture about how Open Publishing systems can be structured with incentives aligned to the best interests of the progress of science.

Web viewers for fMRI

Wed, 25 Jul 2018 00:00:00 +0000

Sharing MRI data with colleagues can be a time-consuming exercise. The files are often large and data-sets need to be viewable in a flexible fashion. Rich features assist the communication of results, including:

3D viewing
flexible slicing
overlay of specific volumes

While there are many software packages for running on the desktop, there’s nothing better than being able to point to a simple HTML link and open the scan data in a prepared format. Therefore, I went digging for an open-source package or library to display MRI renders and slices.

ASSC 22 Conference

Tue, 26 Jun 2018 00:00:00 +0000

Poster for ASSC 22

Below is the poster I will be presenting at the conference, it’s a metaphysical take on consciousness theory, which hopefully will trigger some debate.

please be patient while it loads, it’s a big SVG image!

Markdown tables in LaTeX

Sat, 24 Feb 2018 00:00:00 +0000

LaTeX is a fantastic way to create and display print-ready scientific documents. There are a number of different ways to edit and produce LaTeX documents, which we’ll revist in a future post. In this post, I want to deal with one of the major issues that people find difficult with LaTeX: tables.

LaTeX can certainly produce any type of table you’d like to create, but it does so in a way that can be very difficult to follow visually.

Building Sites With Hugo

Tue, 21 Nov 2017 00:00:00 +0000

In the process of building a new personal website, I hunted around for static website engines. My previous website used an engine called habari, but development of the Habari Project is discontinued and I was interested in writing posts in markdown instead of plain HTML.

So let’s get a few questions answered immediately:

Why a static engine?
What is markdown?

A static website engine converts an intermediate syntax into HTML. It does this as a “static” page, which means that everything the site needs to function is prebuilt. This has three main advantages:

Life Sciences Database

Tue, 17 Oct 2017 00:00:00 +0000

If you’ve ever noticed the 3D images of brain structures on Wikipedia, you may have been curious where they are sourced from.

It turns out that they are generated from a freely accessible Japanese database, the Life Sciences Database Archive. This database is licensed under Creative Commons.

It includes anatomical models that can be downloaded as well as other public databases including gene expression databases. The anatomical models can be downloaded and browsed online at the Body Parts 3D site.

Time in Tokyo Symposium Talk

Tue, 17 Oct 2017 00:00:00 +0000

I recently attended a great symposium for time researchers in Tokyo. It was a fantastic to have a chance to exchange thoughts about new theories of psychological time and to see some very elegant experiments. The conference website is here: Time in Tokyo Symposium.

For the Symposium, I prepared a theoretical discussion of the specious present, considering how we may explore neurophenomenology with reference to recent neuroscientic findings. The slides for the talk are available here:

Experiments with NDVI

Tue, 04 Aug 2015 00:00:00 +0000

NDVI is an acronym for Normalised Difference Vegetation Index. It’s a very interesting measure of plant photosynthesis and health derived from measuring the difference in near-infrared and visual reflectance. I’ve recently been exploring its use for plant monitoring; here are a few calibration images.

[NDVI=\frac{NIR-VIS}{NIR+VIS}]

The original image is on the left, with NDVI on the right

These images were shot using a full-spectrum modified Sony A7 camera with OM Zuiko 21mm/3.5 Lens and Schott BG3 filter at ISO 100, F11, 1/50 to 1/120 sec exposure.

London Musings

Mon, 13 Jul 2015 00:00:00 +0000

Displaying fMRI images in 3D on the web using three.js

Wed, 03 Sep 2014 00:00:00 +0000

Publishing fMRI results usually involves the presentation of slice images that show regions of increased BOLD (Blood Oxygen Dependent Signal). However, fMRI data is inherently three dimensional and often it is difficult to visualise or appropriately present data in 2D formats.

Therefore, it can be useful to implement a method for displaying graphics in 3D form. Luckily, there are some good javascript libraries that interact with the HTML5 canvas attribute to present 3D objects.

Arduino High Speed Digital Acquisition

Wed, 03 Jul 2013 00:00:00 +0000

Psychophysics experiments often require passing messages and signals between different computers and devices. There are a number of methods that are generally used and the limitations of these methods are often a source of consternation for researchers. Experiments designed to probe human temporal perception are particularly sensitive to timing errors in the apparatus. Therefore we have been developing a high resolution signal acquisition device for sending and receiving signals and doing some basic processing.

Arduino I/O and Dynamic Graphing with R and the Manipulate library

Wed, 03 Jul 2013 00:00:00 +0000

Recently, our lab has been working on a general timing measurement system to ensure that psychophysical timing of experiments is valid with different experimental setups ranging from calibrated lab CRT monitors to LCD projectors in MRI facilities.
Essentially, we aim to have a portable and easy to use recorder of digital and analogue signals that can be analysed for delays in hardware and software as well as jitter in various parameters. Our sensors will be signals from eye trackers, photodiodes on displays and manual responses as well as synchronised triggers sent to and from MRI and MEG machines.

Feeling Refined

Sun, 06 Mar 2011 00:00:00 +0000

Mon, 01 Jan 0001 00:00:00 +0000

Personal Health Tracking

A Security Conscious Implementation

Contact

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