Nathan Day
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nthndy.bsky.social
Nathan Day
@nthndy.bsky.social
730 followers 560 following 18 posts
cell biology // image analysis // deep learning // object tracking
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I'm working on the single-cell heterogeneity of Tuberculosis infection at The Francis Crick Institute
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nthndy.bsky.social
working on something fun, interactive AND informative! 🤓 #scicomm #science #tuberculosis #microscopy #imageanalysis
A laptop with a scientific figure open on the screen, displaying fluorescent microscopy images of green human macrophages infected with magenta Mycobacterium tuberculosis bacteria. The manuscript is being prepared as an interactive HTML with pop up images and videos. The laptop rests on a patterned blanket, and two fluffy cats, one grey and one cream-colored, are snoozing nearby. A bookshelf filled with books is visible in the background, along with a wooden floor and some household items.
February 26, 2025 at 10:41 AM
nthndy.bsky.social
Binky wears glasses now
Me holding my old glasses up in front of my cat so that it looks like she is wearing them 😭😭😭
December 4, 2024 at 9:56 PM
nthndy.bsky.social
Some of my favourite scientific images are made in error- here I wanted a visual outline for my segmented macrophages and apparently ran into what I think is a bit-depth error, so it cycles over 256 grayscale values then repeats #science #art #sciart
This image appears to show a black background with irregular, white outlined shapes clustered in horizontal bands across the canvas. The shapes resemble organic cell-like forms (IPSD-Macrophages), each distinct but closely packed together, forming patterns of connected yet individual boundaries. The image has a repetitive, structured arrangement with three horizontal bands of these cell-like outlines, creating a visually layered effect. The outlines are thin and continuous, giving the impression of a network or mosaic of cells seen under a microscope. The alternating dark and light contrast accentuates the outlines, enhancing the cellular-like appearance.
November 15, 2024 at 12:44 PM
nthndy.bsky.social
Here's a photo I took during my PhD: an MDCK monolayer engaging in cell competition between the wild type population (green H2B nuclei marker) and RasV12 mutant (magenta H2B nuclei marker). You can see the RasV12 cells being apically extruded and ejected from the monolayer in the bright regions🌞👽🔬🤔
A microscopy image of a sheet of colourful, flourescently tagged cells. The different colours (described in the original tweet) represent whether the cell is healthy or mutated. There is also a third colour visible in some nuclei, a cyan coloured mottled pattern that shows the localisation of PCNA within the cells nucleus. This can be used to see how the cell is progressing through the cell cycle as the pattern of expression changes in each phase of the cell cycle. At the moment, the PCNA looks like the kodama characters featured in the classic Studio Ghibli film, Princess Mononoke. I.e. like ghostly little figures with different sized eyes looking at you curiously. I love adding alt text lol.
September 1, 2023 at 1:37 PM
nthndy.bsky.social
SEGMENTERROR
A chaotically colourful picture of different blobs all squished together with different coloured concentric rings, with some of the blobs featuring heterogenously shaped blobs within. This image was created by accidently stacking together the output of a segmentation approach with a range of different default cell diameters.
August 22, 2023 at 11:24 AM
nthndy.bsky.social
here's what I'm working on rn: quantifying the heterogeneity of Tuberculosis infection. This necessitates the single-cell tracking of host macrophages in timelapse microscopy data. The tracks shown here are colour coded according to infection status using #btrack #napari #python #tb #cells #biology
a 3D representation of the location of infected macrophage cells over time, from a timelapse microscopy acquisition. The time axis is projected as the z axis whilst the final frame of the timelapse occupies the xy plane. The final frame of the timelapse is a microscopy image showing hundreds of green macrophage cells with intermittent collections of intracellular purple coloured Mtb within. The tracks look like wiggly tails originating from the microscopy image and are coloured purple if the cell is infected with Mtb and white if it is uninfected (or Mtb has not yet been detected).
August 17, 2023 at 12:09 PM
nthndy.bsky.social
A MIS-RENDERING OF SOME TIME-LAPSE TB DATA: I accidentally toggled the 3D display in napari which projected the time axis over z. By pseduocolouring and tilting, you can visualise Mycobacterium tuberculosis growth as sinister, cloud-like volumes that coalesce over time. But why the heterogeneity?
Funky green and pink image with streaks of white throughout. It technically shows the growth Mycobacterium tuberculosis colonies as columns of whispy, cloud-like structures that coalesce over time, which is represented as height in this tilted 3D image snapshot. The scale bars are shown as 3D projections along the bottom. This image was not meant to be anything more than a fun visual representation of Mtb growth!
August 16, 2023 at 2:39 PM