Discover and read the best of Twitter Threads about #bioimageanalysis
Most recents (9)
QuPath v0.4.0 is now available!
Download it at qupath.github.io
#opensource #bioimageanalysis #digitalpathology #java #javafx
Download it at qupath.github.io
#opensource #bioimageanalysis #digitalpathology #java #javafx
There are so many new things that it'll take some days to describe even just the main ones.
For now, I'll start by mentioning a few of the user interface improvements.
QuPath v0.4.0 is more welcoming than previous versions... and a bit more stylish.
For now, I'll start by mentioning a few of the user interface improvements.
QuPath v0.4.0 is more welcoming than previous versions... and a bit more stylish.
In fact, you can even style it in your own unique way if you really want to, thanks to #javafx & css (ideally in a nicer way than in my screenshots).
qupath.readthedocs.io/en/0.4/docs/re…
qupath.readthedocs.io/en/0.4/docs/re…
If you want to learn about #bioimageanalysis I've written a free & open textbook that tries to help:
bioimagebook.github.io
Thanks to the wonder of @ExecutableBooks & other modern magic it's not quite like a normal book... (thread)
@OpenEdEdinburgh @NEUBIAS_COST @BioimagingNA
bioimagebook.github.io
Thanks to the wonder of @ExecutableBooks & other modern magic it's not quite like a normal book... (thread)
@OpenEdEdinburgh @NEUBIAS_COST @BioimagingNA
First, the book tries to cover the main concepts, independently of any software, in a practical way.
This includes common pitfalls & problems, like data clipping, that can doom analysis from the start (2/n)
This includes common pitfalls & problems, like data clipping, that can doom analysis from the start (2/n)
It also includes tricky stuff important for a lot of microscopy image analysis, like noise distributions & the signal-to-noise ratio... (3/n)
Excited to introduce #3DRCAN for denoising, super resolution and expansion microscopy. Super proud of this colab with Hari Shroff, Jiji Chen et al.
@NIBIBgov @arpcomplex
Preprint: biorxiv.org/content/10.110…
Code: github.com/AiviaCommunity…
#microscopy #aimicroscopy #aivia
1/17
@NIBIBgov @arpcomplex
Preprint: biorxiv.org/content/10.110…
Code: github.com/AiviaCommunity…
#microscopy #aimicroscopy #aivia
1/17
"Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes"
J Chen, H Sasaki, H Lai, Y Su, J Liu, Y Wu, A Zhovmer, C Combs, I Rey-Suarez, H Chang, C Huang, X Li, M Guo, S Nizambad, A Upadhyaya, J Lee, L Lucas, H Shroff.
2/17
J Chen, H Sasaki, H Lai, Y Su, J Liu, Y Wu, A Zhovmer, C Combs, I Rey-Suarez, H Chang, C Huang, X Li, M Guo, S Nizambad, A Upadhyaya, J Lee, L Lucas, H Shroff.
2/17
We are particularly interested in characterizing the limits of #deeplearning based approaches to image restoration. You will find several experiments comparing several best-in-class approaches: #3DRCAN, #CARE, #SRResNet and #ESRGAN.
#microscopy #aimicroscopy #iSIM
3/17
#microscopy #aimicroscopy #iSIM
3/17
@QuPath #tweetorial part 2... this time it's (almost) all annotations. 1/20
#bioimageanalysis #digitalpathology #opensource #javafx
#bioimageanalysis #digitalpathology #opensource #javafx
I say 'almost all', because I need to mention the command list early: with 'Ctrl + L' you get a searchable list of everything in the menus.
Having told you that, I can now ignore the menus & focus on shortcuts - safe in the knowledge you can find things if you need them. 2/20
Having told you that, I can now ignore the menus & focus on shortcuts - safe in the knowledge you can find things if you need them. 2/20
(If you *really* like the command list, you can turn it into a command bar and give it a special place at the top of the viewer... but I probably wouldn't unless I broke my 'L' key.) 3/20
Time for a quick introduction to @QuPath in tweetorial form.
First up: a little background on how QuPath differs from other great #opensource tools for #bioimageanalysis like @FijiSc & @CellProfiler - and how to get started viewing images. 1/12
qupath.github.io
First up: a little background on how QuPath differs from other great #opensource tools for #bioimageanalysis like @FijiSc & @CellProfiler - and how to get started viewing images. 1/12
qupath.github.io
QuPath's most obvious distinguishing feature is that it handles whole slide images. These are ultra-large 2D images, often up to 50 GB in size.
Whole slide images are everywhere in #digitalpathology & increasingly common in research. 2/12
Whole slide images are everywhere in #digitalpathology & increasingly common in research. 2/12
A single whole slide image can be more than 200k x 100k pixels in size & contain a huge amount of information that matters to researchers & clinicians.
The trouble is trying to wring that information out of billions of pixels. 3/12
The trouble is trying to wring that information out of billions of pixels. 3/12
@3dtrevor @Mariposa_Rising @MascalchiP and the wider team are running another well attended hands on online #bioimageanalysis workshop. Today about 3d segmentation and tracking! See more: drvtechnologies.com/aivia-online-w… #aivia #aimicroscopy #Microscopy
Uses the freely available #aiviaweb.
Setting ROIs to get quick previews.
It's tomorrow! We have developed a solution to run full online workshops. We will use #aiviaweb and a few other tools to make it happen. You will see a brief talk/intro, then use your own AiviaWeb to complete several #bioimageanalysis exercises with the help of the Aivia team.1/3
Two events per week (one US one EU). drvtechnologies.com/aivia-online-w…
US:
15 of April: Create video animations with Aivia Community
22 of April: Neuron analysis
29 of April: Pixel classifier
6 of May: Detecting and tracking objects in 3D
13 of May: Image analysis with Python in Aivia
2/3
US:
15 of April: Create video animations with Aivia Community
22 of April: Neuron analysis
29 of April: Pixel classifier
6 of May: Detecting and tracking objects in 3D
13 of May: Image analysis with Python in Aivia
2/3
As this will be a real time hands on experience (just like if you were in a room with us, each of you with your own Aivia computer), there will be several of us on hand to help out! Quyen and Hoyin too - not twitter for now. 3/3
We will start to roll out #AiviaWeb at no cost to use, tomorrow. All #aivia functionality accessible via a web browser. This is part of our #covid19 mitigation plan - more actions soon so you can continue to be productive while #wfh. #bioimageanalyis #aiviacommunity #microscopy
Once you are signed up we will reach out to you with all the details including usage and booking guidelines. A webpage dedicated to our covid19 / wfh mitigation plan will be up very soon too. Many more resources are in the pipeline.
*** 1/9 ***
Today is HIS-TO-RI-CAL about Aivia!!!
We are releasing a free to use software called Aivia Community
It’s meant to be a collaborative tool, allowing you to…
(see next tweets)
#Microscopy #ImageAnalysis #bioimageanalysis #3Drendering
Today is HIS-TO-RI-CAL about Aivia!!!
We are releasing a free to use software called Aivia Community
It’s meant to be a collaborative tool, allowing you to…
(see next tweets)
#Microscopy #ImageAnalysis #bioimageanalysis #3Drendering
*** 2/9 ***
Open and interactively explore 2-to-5D microscopy data sets
(tested up to 3 TB files)
Open and interactively explore 2-to-5D microscopy data sets
(tested up to 3 TB files)
*** 3/9 ***
Create attractive visual outputs (such as snapshots, video animation) from:
•raw microscopy images
•OR data sets previously analyzed with Aivia (with 3D surfaces, traced neurons for instance)
#3Drendering #Animations #VideoExport #Snapshots #3Dsurfaces
Create attractive visual outputs (such as snapshots, video animation) from:
•raw microscopy images
•OR data sets previously analyzed with Aivia (with 3D surfaces, traced neurons for instance)
#3Drendering #Animations #VideoExport #Snapshots #3Dsurfaces
