Lmst

Image analysts: What is your go to method for batch converting image files from the proprietary format to a tiff file? If this should be done at all...

I’ve been using FIJI to open and re-save mine. Although this gives me another look at the image as a QC step, I am using Napari more and more and have found a tiff easier to load into Python.

#Microscopy #ImageAnalysis #Napari #FIJI

We manage to introduce a pipeline mixing spatialdata, #scPRINT #HEST1K #CONCH #SPATIALDATA and #NAPARI. Our first POC was STsimilarity: finding similar image patches across a large database of histopatologic slides.
2/6

Glad to join the Crick Bioimage Analysis Symposium for the second time (first in person!). Looking forward to two days of cool science, analyses, and technologies! @thecrick

#CBIAS2024 #ImageAnalysis #Bioinformatics #napari #pathology #pathomics

Intro slide for CBIAS 2024 at the Crick. David Barry is standing in front of the audience and talking about a slide with a QR for the programme.

Started work on maybe the first real enhancement to #yt_napari that might be useful to the #napari community at large by adding the ability to export image layers from napari to a yt dataset. Currently putting to it to use by building a little widget for yt's PhasePlot (a 2D binned statistic with optional weighting) that lets you select from available layers and get back a nice plot. Still lots of UI improvements to do... but it's a start!

#python #foss #opensource #DataVis

Screen shot of the napari GUI that shows a 3d multichannel image from napari's sample datasets (something related to cells... I don't know, I'm not a biologist...). The middle of the image shows a 3d views of cell structures. The right side of the image shows a new PhasePlot widget that includes drop down menus for selecting the x, y and z arguments for a 2D binned and weighted histogram along with a resulting 2D weighted histogram below.

#OpenSIMMO: A fully-automated #OpenSource multicolour structured illumination module for #SuperResolution #microscopy:

-#fluorescence #microscope add-on
-#RasPi/#ESP32 control

Preprint: https://doi.org/10.1101/2024.07.04.601961
Web: https://opensimmo.github.io/
#DIYbio #lab #instruments #SIM #imaging #laser #optics #Napari #Python #ImSwitch #DMD #OpenUC2

Started work on a new PR to yt-napari to add some of yt's sample datasets to napari's Open Sample menu! Seems to be working, still some tests to write and some design decisions to be made... but here's a pretty video.

code: https://github.com/data-exp-lab/yt-napari/pull/149

video: sample data is the GalaxyClusterMerger sample dataset for the #flash frontend.

#yt #yt-napari #napari #astro #astroviz #3dvis #3d #OpenSource #python

it took longer than i care to admit to revisit Talley Lambert's revised pattern for the Pulser's library: https://github.com/kephale/pulser/blob/main/example.py

but i finally have a significant need to use this for a bespoke annotation tool. such an easy pattern to extend.

#python #midi #hci #napari

Interesting new #preprint about #tissueclearing and #lightsheet #microscopy in mouse ovaries. Complete with #napari-based deep-learning pipeline and detailed build instructions for 3D-printed sample chambers for solvent-cleared samples, so they can be viewed under a #confocal!

OoCount: A machine-learning based approach to mouse ovarian follicle counting and classification
Folts et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.05.13.593993v1

Fig. 3: Mounting and preparing adult ovaries for imaging. 1. Print a coverslip'n'slide and gather materials for mounting the samples. Note the fillinf inlets on the coverlip'n'slide indicated with the blue arrows. 2. Apply super glue around the edges of a coverlslip and attach it to the the coverslip'n'slide. 3. Load syringe with sealant for more precise control over application. 4. Using the syringe, create a chamber using sealant by lining the edges of the coverslip. 5. Arrange the samples on the coverslip. 6. Apply a coverslip to the top of the sealant, creating a chamber. 7. Gently push on the top coverslip until it touches the samples. 8. Using a pipet, fill the chamber with ECi. 9. Plug the filling inlets with sealant. 10. Allow to cure for 1h before imaging.

Preprint describing Nellie, a napari plugin for automated organelle segmentation. Results look impressive!

https://arxiv.org/abs/2403.13214

repo (with video): https://github.com/aelefebv/nellie

#CellBiology #microscopy #napari

The #neuroscience Mastodon hive-mind worked wonderfully earlier - let’s try again!

In #napari, I have loaded a video using the `napari-video` plugin. I would like to get some simple image statistics for all frames in the video - does anyone know how to? I have looked through the various plug-ins, but none seem obvious… but it’s so simple (no segmentation, nothing complicated), I feel like I must be missing something!

#PyTME: A fast, flexible & multi-purpose template matching library for #cryoEM data:

-#OpenSource
-HT mining of cryoEM & ET datasets
-multi #CPU/#GPU support
-#Napari plugin

https://doi.org/10.1016/j.softx.2024.101636
#CompChem #bioinformatics #DIYbio #lab #instruments #microscopy #imaging #Python

Inspired by https://twitter.com/hisadan/status/1699354785441571323?s=20.
Tooted from #napari with #tootapari.

A screenshot automatically generated with tootapari. The corresponding toot is: Inspired by https://twitter.com/hisadan/status/1699354785441571323?s=20.
Tooted from #napari with #tootapari..

Playing with an adaptation of the processing code here (https://twitter.com/hisadan/status/1697878658437054785?s=20) to napari.
Tooted from #napari with #tootapari.

A screenshot automatically generated with tootapari. The corresponding toot is: Playing with an adaptation of the processing code here (https://twitter.com/hisadan/status/1697878658437054785?s=20) to napari.
Tooted from #napari with #tootapari..

I livestreamed these blobs here: https://mastodon.social/@couldabeenscience@botsin.space. The #napari hackathon is done and was a success!

Having a ton of fun utilizing other plugins with yt-napari. This video shows some interactive plotting with napari-clusters-plotter after I used it to run a kmeans classification of individual pixels across 3 image layers (2D samples through yt's IsolatedGalaxy test data set).

Full description will be up on youtube soon (final installment of the yt-napari tutorial series!).

#yt-project #yt_astro #DataVisualization #napari @napari