Talley Lambert
@talley.codes
Microscopist & Python developer at Harvard Med. Creator @fpbase.org
Just played a bit with ty docs.astral.sh/ty/
I’m drooling anticipating the day when the last slow pre-commit hook (mypy/pyright) falls and the entire check is blazing fast ⚡️💨
Maybe not just yet… but so soon
I’m drooling anticipating the day when the last slow pre-commit hook (mypy/pyright) falls and the entire check is blazing fast ⚡️💨
Maybe not just yet… but so soon
ty
ty is an extremely fast Python type checker.
docs.astral.sh
September 26, 2025 at 1:09 AM
Just played a bit with ty docs.astral.sh/ty/
I’m drooling anticipating the day when the last slow pre-commit hook (mypy/pyright) falls and the entire check is blazing fast ⚡️💨
Maybe not just yet… but so soon
I’m drooling anticipating the day when the last slow pre-commit hook (mypy/pyright) falls and the entire check is blazing fast ⚡️💨
Maybe not just yet… but so soon
ugh. the macos Tahoe border radius is killing me
September 22, 2025 at 2:50 PM
ugh. the macos Tahoe border radius is killing me
it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io)
but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂
as a mild deutan myself, I appreciate it! 🙏
but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂
as a mild deutan myself, I appreciate it! 🙏
July 5, 2025 at 8:28 PM
it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io)
but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂
as a mild deutan myself, I appreciate it! 🙏
but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂
as a mild deutan myself, I appreciate it! 🙏
i'm generally thrilled with gh copilot agent recently.
There have been multiple very funny cases though where I have asked it to fix a broken test, and the "fix" came in the form of simply deleting the problematic test 😂
"well ... the tests PASS now don't they??"
There have been multiple very funny cases though where I have asked it to fix a broken test, and the "fix" came in the form of simply deleting the problematic test 😂
"well ... the tests PASS now don't they??"
June 16, 2025 at 8:49 PM
i'm generally thrilled with gh copilot agent recently.
There have been multiple very funny cases though where I have asked it to fix a broken test, and the "fix" came in the form of simply deleting the problematic test 😂
"well ... the tests PASS now don't they??"
There have been multiple very funny cases though where I have asked it to fix a broken test, and the "fix" came in the form of simply deleting the problematic test 😂
"well ... the tests PASS now don't they??"
for you other colorblind coders out there, tired of missing the red X in your github actions logs
.color-fg-danger, .fgColor-danger {color: magenta !important;}
.octicon-x {color: magenta !important;}
you're welcome
.color-fg-danger, .fgColor-danger {color: magenta !important;}
.octicon-x {color: magenta !important;}
you're welcome
May 21, 2025 at 6:32 PM
for you other colorblind coders out there, tired of missing the red X in your github actions logs
.color-fg-danger, .fgColor-danger {color: magenta !important;}
.octicon-x {color: magenta !important;}
you're welcome
.color-fg-danger, .fgColor-danger {color: magenta !important;}
.octicon-x {color: magenta !important;}
you're welcome
Reposted by Talley Lambert
Steven has our Snouty-OPM running again after our lab move. He added projection mode, sensorless AO, and a new control GUI based on @talley.codes + crew's pymmcore-plus/pymmcore-gui. Here are some IF-labeled microglia (orange) in the middle of an uncleared 60um mouse brain slice. No deconvolution!
April 9, 2025 at 3:43 AM
Steven has our Snouty-OPM running again after our lab move. He added projection mode, sensorless AO, and a new control GUI based on @talley.codes + crew's pymmcore-plus/pymmcore-gui. Here are some IF-labeled microglia (orange) in the middle of an uncleared 60um mouse brain slice. No deconvolution!
Reposted by Talley Lambert
Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...
March 29, 2025 at 2:42 PM
Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...
Reposted by Talley Lambert
💻 Announcing the Boston Bioimage Analysis Course — BoBiAC!
Join us this July at Harvard Medical School in Boston for a 6-day deep dive into bioimage analysis with Python, hosted by the IAC and CITE.
Apply by May 16th, 2025!
Join us this July at Harvard Medical School in Boston for a 6-day deep dive into bioimage analysis with Python, hosted by the IAC and CITE.
Apply by May 16th, 2025!
March 24, 2025 at 6:41 PM
💻 Announcing the Boston Bioimage Analysis Course — BoBiAC!
Join us this July at Harvard Medical School in Boston for a 6-day deep dive into bioimage analysis with Python, hosted by the IAC and CITE.
Apply by May 16th, 2025!
Join us this July at Harvard Medical School in Boston for a 6-day deep dive into bioimage analysis with Python, hosted by the IAC and CITE.
Apply by May 16th, 2025!
This document rom the griffe docs is *awesome*. Basically a missing manual on designing the public API for your Python package: extremely well written, with good tips for beginners and advanced devs alike.
mkdocstrings.github.io/griffe/guide...
mkdocstrings.github.io/griffe/guide...
Public APIs - Griffe
Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API.
mkdocstrings.github.io
February 5, 2025 at 11:53 PM
This document rom the griffe docs is *awesome*. Basically a missing manual on designing the public API for your Python package: extremely well written, with good tips for beginners and advanced devs alike.
mkdocstrings.github.io/griffe/guide...
mkdocstrings.github.io/griffe/guide...
If you use mkdocs for your python docs, and want quick full API autogen (with navigation) try
github.com/tlambert03/m...
Particularly if you currently use the mkdocs-gen-files/literatenav/custom-script approach
github.com/tlambert03/m...
Particularly if you currently use the mkdocs-gen-files/literatenav/custom-script approach
GitHub - tlambert03/mkdocs-api-autonav
Contribute to tlambert03/mkdocs-api-autonav development by creating an account on GitHub.
github.com
February 5, 2025 at 11:11 PM
If you use mkdocs for your python docs, and want quick full API autogen (with navigation) try
github.com/tlambert03/m...
Particularly if you currently use the mkdocs-gen-files/literatenav/custom-script approach
github.com/tlambert03/m...
Particularly if you currently use the mkdocs-gen-files/literatenav/custom-script approach
Reposted by Talley Lambert
Join me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott for our two week CSHL course on microscopy & image analysis starting March 24, 2025! Applications are due 1/31/25. meetings.cshl.edu/courses.aspx...
Quantitative Imaging: From Acquisition to Analysis
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
January 7, 2025 at 6:42 PM
Join me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott for our two week CSHL course on microscopy & image analysis starting March 24, 2025! Applications are due 1/31/25. meetings.cshl.edu/courses.aspx...
Reposted by Talley Lambert
😱📣 BlueSky-ers: WE NEED YOUR HELP!!! 🙏
All of you who ever liked a lecture of mine...
All of you who liked one of the courses I teach in...
All of you I work(ed) with in one way or another...
All of you who see my desperation! 😜
PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...
All of you who ever liked a lecture of mine...
All of you who liked one of the courses I teach in...
All of you I work(ed) with in one way or another...
All of you who see my desperation! 😜
PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...
Postdocs in Artificial Intelligence
Human Technopole (HT) is an interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health
careers.humantechnopole.it
October 27, 2023 at 3:05 PM
😱📣 BlueSky-ers: WE NEED YOUR HELP!!! 🙏
All of you who ever liked a lecture of mine...
All of you who liked one of the courses I teach in...
All of you I work(ed) with in one way or another...
All of you who see my desperation! 😜
PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...
All of you who ever liked a lecture of mine...
All of you who liked one of the courses I teach in...
All of you I work(ed) with in one way or another...
All of you who see my desperation! 😜
PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...
Reposted by Talley Lambert
Finally got around to creating a basic Python wrapper for the FPbase API. Hope it helps for those wanting to programmatically retrieve data from FPbase using Python.
pip install fpbase
github.com/tlambert03/f...
pip install fpbase
github.com/tlambert03/f...
GitHub - tlambert03/fpbasepy: Python wrapper for FPBase.org GraphQL API.
Python wrapper for FPBase.org GraphQL API. Contribute to tlambert03/fpbasepy development by creating an account on GitHub.
github.com
November 20, 2024 at 7:42 PM
Finally got around to creating a basic Python wrapper for the FPbase API. Hope it helps for those wanting to programmatically retrieve data from FPbase using Python.
pip install fpbase
github.com/tlambert03/f...
pip install fpbase
github.com/tlambert03/f...
Reposted by Talley Lambert
uv now ships with dedicated documentation for PyTorch
November 19, 2024 at 10:17 PM
uv now ships with dedicated documentation for PyTorch
If you still default to using `os.path`, this one’s for you:
I've updated my new #pathlib article with additional examples, improved wording, and more links to documentation. ✨
One nice thing about finally publishing in text form: #Python folks happily provide (frequently) constructive feedback so I can immediately iterate. 💗
pym.dev/pathlib-module
One nice thing about finally publishing in text form: #Python folks happily provide (frequently) constructive feedback so I can immediately iterate. 💗
pym.dev/pathlib-module
Python's pathlib module
Python's pathlib module is the tool to use for working with file paths. See pathlib quick reference tables and examples.
pym.dev
November 20, 2024 at 3:19 AM
If you still default to using `os.path`, this one’s for you:
Reposted by Talley Lambert
Hello friends! We’re here to celebrate and share all things fluorescent. Tag us as you share findings related to the use or publication of FPs and other probes
November 18, 2024 at 6:29 PM
Hello friends! We’re here to celebrate and share all things fluorescent. Tag us as you share findings related to the use or publication of FPs and other probes
Reposted by Talley Lambert
Doing good science is 90% finding a science buddy to constantly talk to about the project.
November 9, 2024 at 10:53 PM
Doing good science is 90% finding a science buddy to constantly talk to about the project.
I feel I specifically should have done better here. (Talky?? Really Talley?)
November 18, 2024 at 12:35 AM
I feel I specifically should have done better here. (Talky?? Really Talley?)
Reposted by Talley Lambert
Six tips for going public with your lab’s software: https://www.nature.com/articles/d41586-024-03344-y
1) make time for maintenance
2) simplify installation
3) add a GUI or good CLI
4) good documentation
5) use github/git
6) automated testing
Any other tips people have? #softwareengineering
1) make time for maintenance
2) simplify installation
3) add a GUI or good CLI
4) good documentation
5) use github/git
6) automated testing
Any other tips people have? #softwareengineering
October 18, 2024 at 12:18 PM
Six tips for going public with your lab’s software: https://www.nature.com/articles/d41586-024-03344-y
1) make time for maintenance
2) simplify installation
3) add a GUI or good CLI
4) good documentation
5) use github/git
6) automated testing
Any other tips people have? #softwareengineering
1) make time for maintenance
2) simplify installation
3) add a GUI or good CLI
4) good documentation
5) use github/git
6) automated testing
Any other tips people have? #softwareengineering