Brian Northan
@truenorth-ia.bsky.social
Contract Research and Development Engineer, Image Processing. XC skier. Stockade-athon 15 km Running Road Race Director.
I was searching for a Python utility for Fourier Ring/Shell Correlation. All I got in a blue sky search were 4 small posts from @christletx.bsky.social ... all I got from chatgpt was installation instructions for non-existent libraries and github repos... anyone know a good tool for this?
August 16, 2025 at 3:08 PM
I was searching for a Python utility for Fourier Ring/Shell Correlation. All I got in a blue sky search were 4 small posts from @christletx.bsky.social ... all I got from chatgpt was installation instructions for non-existent libraries and github repos... anyone know a good tool for this?
Reposted by Brian Northan
📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
CBIAS napari workshop 2025
crick.ac.uk
August 11, 2025 at 2:26 PM
📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
Reposted by Brian Northan
Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.
August 5, 2025 at 12:38 PM
Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.
Reposted by Brian Northan
The 1st working version of my little @napari.org plugin (napari-czitools) is almost ready.
It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read.
Still quite some things to improve ...
It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read.
Still quite some things to improve ...
July 30, 2025 at 7:50 PM
The 1st working version of my little @napari.org plugin (napari-czitools) is almost ready.
It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read.
Still quite some things to improve ...
It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read.
Still quite some things to improve ...
Reposted by Brian Northan
Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
July 30, 2025 at 8:15 AM
Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8
Pixi and Napari-Easy-augment-Batch-DL
YouTube video by Brian Northan
youtu.be
July 30, 2025 at 5:31 PM
I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8
Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...
GitHub - AlexHego/DL-pixel-classification
Contribute to AlexHego/DL-pixel-classification development by creating an account on GitHub.
github.com
July 21, 2025 at 6:41 PM
Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...
Reposted by Brian Northan
Btw, and in the spirit of #OpenScience, all my #Napari #bioimage analysis #tutorials are freely available — from basics to #segmentation, #tracking, and #clustering. Feel free to explore and share ✌️
🌍 www.fabriziomusacchio.com/teaching/tea...
🌍 www.fabriziomusacchio.com/teaching/tea...
July 13, 2025 at 9:10 PM
Btw, and in the spirit of #OpenScience, all my #Napari #bioimage analysis #tutorials are freely available — from basics to #segmentation, #tracking, and #clustering. Feel free to explore and share ✌️
🌍 www.fabriziomusacchio.com/teaching/tea...
🌍 www.fabriziomusacchio.com/teaching/tea...
Reposted by Brian Northan
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
June 17, 2025 at 8:16 AM
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
Reposted by Brian Northan
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
June 16, 2025 at 3:53 PM
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
Reposted by Brian Northan
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Annotating Images in Cellpose - FocalPlane
Annotating Images in Cellpose - How to
focalplane.biologists.com
June 9, 2025 at 9:43 AM
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Reposted by Brian Northan
Need help with bioimage analysis? Contact the UK Euro-BioImaging Node to see how we can help!
www.eurobioimaging-access.eu/nodes/uk-node
www.eurobioimaging-access.eu/nodes/uk-node
May 30, 2025 at 3:14 PM
Need help with bioimage analysis? Contact the UK Euro-BioImaging Node to see how we can help!
www.eurobioimaging-access.eu/nodes/uk-node
www.eurobioimaging-access.eu/nodes/uk-node
Reposted by Brian Northan
Want to host your own AI models without relying on external infrastructure?
Enter BioEngine
ai4life.eurobioimaging.eu/announcing-b...
Your go-to for flexible, self-hosted bioimage analysis. Open source, scalable, and built for you!
Enter BioEngine
ai4life.eurobioimaging.eu/announcing-b...
Your go-to for flexible, self-hosted bioimage analysis. Open source, scalable, and built for you!
May 27, 2025 at 12:45 PM
Want to host your own AI models without relying on external infrastructure?
Enter BioEngine
ai4life.eurobioimaging.eu/announcing-b...
Your go-to for flexible, self-hosted bioimage analysis. Open source, scalable, and built for you!
Enter BioEngine
ai4life.eurobioimaging.eu/announcing-b...
Your go-to for flexible, self-hosted bioimage analysis. Open source, scalable, and built for you!
I've started a thread on the imagesc forum about how ambiguous labels might affect deep learning models. If you've encountered mislabeled data, strange training artifacts, or examples where the former caused the latter — I'd love to hear your insights. forum.image.sc/t/are-we-see...
Are we seeing downstream effects of ambiguous labelling on new generalist models?
Below is a rather long post about some issues I’ve been seeing in generalist models ‘finding’ and ‘not finding’ objects, and my hypothesis as to why. Love to hear if others are seeing similar. The i...
forum.image.sc
May 27, 2025 at 4:57 PM
I've started a thread on the imagesc forum about how ambiguous labels might affect deep learning models. If you've encountered mislabeled data, strange training artifacts, or examples where the former caused the latter — I'd love to hear your insights. forum.image.sc/t/are-we-see...
Reposted by Brian Northan
We've been trying nnInteractive (github.com/MIC-DKFZ/nap...) to quickly create labeled data for later training an Omnipose model. I whatever black magic you did there, keep at it! It's such a life-changer!
May 16, 2025 at 11:46 AM
We've been trying nnInteractive (github.com/MIC-DKFZ/nap...) to quickly create labeled data for later training an Omnipose model. I whatever black magic you did there, keep at it! It's such a life-changer!
Reposted by Brian Northan
Reminder: if you go to the GloBIAS conference we can help you contribute to napari at the hackathon! A bunch of the team will be there! (Great thanks to the GloBIAS team for accommodating us!!!)
More details on the conference website.
More details on the conference website.
Deadlines extended - you can still register for the GloBIAS conference! We have extended most deadlines. Please check our webpage: tinyurl.com/mr3kx5a5! Looking forward to welcoming you to Kobe, for training, developing and discussing a broad range of BIA topics!
May 16, 2025 at 8:11 AM
Reminder: if you go to the GloBIAS conference we can help you contribute to napari at the hackathon! A bunch of the team will be there! (Great thanks to the GloBIAS team for accommodating us!!!)
More details on the conference website.
More details on the conference website.
Reposted by Brian Northan
Episode 5 - sure, most cells have one nucleus, but what happens when they DON'T? @erinweisbart.bsky.social and I try to get to the bottom of what on earth you can do when your cells and nuclei just don't match up on the latest episode of "Ask Erin/Dear Beth"
May 15, 2025 at 5:21 PM
Episode 5 - sure, most cells have one nucleus, but what happens when they DON'T? @erinweisbart.bsky.social and I try to get to the bottom of what on earth you can do when your cells and nuclei just don't match up on the latest episode of "Ask Erin/Dear Beth"
This is a nice overview of normalization techniques which are very important for deep learning training. It is pretty common that differences in the training and testing image intensity ranges lead to unpredictable errors so learning to troubleshoot normalization issues is very useful.
Image normalization: trivial enough to automate, impactful enough to quietly sabotage your results.
Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome.
👇
haesleinhuepf.github.io/BioImageAnal...
Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome.
👇
haesleinhuepf.github.io/BioImageAnal...
Image Normalization — Bio-image Analysis Notebooks
haesleinhuepf.github.io
May 16, 2025 at 10:53 AM
This is a nice overview of normalization techniques which are very important for deep learning training. It is pretty common that differences in the training and testing image intensity ranges lead to unpredictable errors so learning to troubleshoot normalization issues is very useful.
Reposted by Brian Northan
Just uploaded a simple script to run cellpose for cell segmentation on two-photon calcium imaging data and extract ΔF/F traces. It runs slower without a GPU, but still works well. Check it out and give it a try!
github.com/dav1dcg/neur...
github.com/dav1dcg/neur...
neuro-notebook-templates/Notebooks/cellpose_segmentation_2p.ipynb at main · dav1dcg/neuro-notebook-templates
Jupyter notebook templates for processing and analyzing neuroscience data. - dav1dcg/neuro-notebook-templates
github.com
May 11, 2025 at 6:21 PM
Just uploaded a simple script to run cellpose for cell segmentation on two-photon calcium imaging data and extract ΔF/F traces. It runs slower without a GPU, but still works well. Check it out and give it a try!
github.com/dav1dcg/neur...
github.com/dav1dcg/neur...
Reposted by Brian Northan
We are proudly hosting
𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School):
𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦
When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time)
Join us on Zoom! harvard.zoom.us/j/9762343464...
𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School):
𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦
When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time)
Join us on Zoom! harvard.zoom.us/j/9762343464...
May 7, 2025 at 3:59 PM
We are proudly hosting
𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School):
𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦
When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time)
Join us on Zoom! harvard.zoom.us/j/9762343464...
𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School):
𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦
When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time)
Join us on Zoom! harvard.zoom.us/j/9762343464...
Reposted by Brian Northan
💻 Apply to our beginner-friendly Boston Bioimage Analysis Course!
Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required!
Fee waivers available thanks to funding from @bioimagingna.bsky.social!
🗓️ Apply June 1st!
iac.hms.harvard.edu/bobiac/2025/
Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required!
Fee waivers available thanks to funding from @bioimagingna.bsky.social!
🗓️ Apply June 1st!
iac.hms.harvard.edu/bobiac/2025/
May 8, 2025 at 2:39 PM
💻 Apply to our beginner-friendly Boston Bioimage Analysis Course!
Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required!
Fee waivers available thanks to funding from @bioimagingna.bsky.social!
🗓️ Apply June 1st!
iac.hms.harvard.edu/bobiac/2025/
Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required!
Fee waivers available thanks to funding from @bioimagingna.bsky.social!
🗓️ Apply June 1st!
iac.hms.harvard.edu/bobiac/2025/
Reposted by Brian Northan
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try!
nimbusimage.com
nimbusimage.com
May 7, 2025 at 6:19 PM
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try!
nimbusimage.com
nimbusimage.com
Reposted by Brian Northan
Want to learn more about bioimage analysis and how to think like a bioimage analyst? Check out our bootcamp- applications close next week!
BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
May 5, 2025 at 11:35 AM
Want to learn more about bioimage analysis and how to think like a bioimage analyst? Check out our bootcamp- applications close next week!
Reposted by Brian Northan
So excited and proud of everyone! 🎉 With this release I worked very hard to contribute to napari and learned so much along the way. I guess they want to keep me around, as I'm a core dev now! 🥳 Grateful for the entire image analysis community. 🥰
And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵
a woman in a hat is crying and says " i 've traveled a good many miles to get here "
Alt: Charlotte from the Sanditon TV series, emotionally exclaiming, "I've traveled a good many miles to get here!"
media.tenor.com
May 1, 2025 at 2:24 PM
So excited and proud of everyone! 🎉 With this release I worked very hard to contribute to napari and learned so much along the way. I guess they want to keep me around, as I'm a core dev now! 🥳 Grateful for the entire image analysis community. 🥰
Reposted by Brian Northan
In case you were wondering where the "Tools" menu is gone in @napari.org 0.6.0, please update your environment using "pip install napari-assistant==0.6.0". Then just start "naparia" instead of "napari" from the terminal, while we are working on a better solution.
github.com/haesleinhuep...
github.com/haesleinhuep...
May 2, 2025 at 9:58 AM
In case you were wondering where the "Tools" menu is gone in @napari.org 0.6.0, please update your environment using "pip install napari-assistant==0.6.0". Then just start "naparia" instead of "napari" from the terminal, while we are working on a better solution.
github.com/haesleinhuep...
github.com/haesleinhuep...