Talley Lambert
@talley.codes
Microscopist & Python developer at Harvard Med. Creator @fpbase.org
well, I'm biased... but i think absolutely! 😂
WAY more things in the database (like 1000s more). more FPs, dyes, filters from all providers. (The thermo viewer is primarily their own products). share/restore/download state.
plus, it's open source, non-commercial, and accepts contribs
try it? 👍
WAY more things in the database (like 1000s more). more FPs, dyes, filters from all providers. (The thermo viewer is primarily their own products). share/restore/download state.
plus, it's open source, non-commercial, and accepts contribs
try it? 👍
November 5, 2025 at 3:12 PM
well, I'm biased... but i think absolutely! 😂
WAY more things in the database (like 1000s more). more FPs, dyes, filters from all providers. (The thermo viewer is primarily their own products). share/restore/download state.
plus, it's open source, non-commercial, and accepts contribs
try it? 👍
WAY more things in the database (like 1000s more). more FPs, dyes, filters from all providers. (The thermo viewer is primarily their own products). share/restore/download state.
plus, it's open source, non-commercial, and accepts contribs
try it? 👍
Indeed! Was broken. Fixed now
November 4, 2025 at 10:17 PM
Indeed! Was broken. Fixed now
It’s actually neither, it’s np.zer<TAB>
October 9, 2025 at 10:38 PM
It’s actually neither, it’s np.zer<TAB>
there quite a bit of `@Todo` in my checks still
September 29, 2025 at 10:38 PM
there quite a bit of `@Todo` in my checks still
Excellent! Thoroughly enjoyed.
(And it was cool to learn where the inspiration for your cmap PRs came from 😄… nice integration!)
(And it was cool to learn where the inspiration for your cmap PRs came from 😄… nice integration!)
September 26, 2025 at 2:34 AM
Excellent! Thoroughly enjoyed.
(And it was cool to learn where the inspiration for your cmap PRs came from 😄… nice integration!)
(And it was cool to learn where the inspiration for your cmap PRs came from 😄… nice integration!)
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! 🙏
Gotcha. That sounds nice!
I’ve definitely been very happy with gh copilot agent as well, particularly with sonnet 4. my comment was as much about the humorous failure modes :)
I’ve definitely been very happy with gh copilot agent as well, particularly with sonnet 4. my comment was as much about the humorous failure modes :)
June 17, 2025 at 9:05 PM
Gotcha. That sounds nice!
I’ve definitely been very happy with gh copilot agent as well, particularly with sonnet 4. my comment was as much about the humorous failure modes :)
I’ve definitely been very happy with gh copilot agent as well, particularly with sonnet 4. my comment was as much about the humorous failure modes :)
Wouldn’t that depend as much (if not more) on the underlying model than the agent extension?
June 17, 2025 at 6:51 PM
Wouldn’t that depend as much (if not more) on the underlying model than the agent extension?
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??"
I think there’s a good degree of personal preference and subjectivity here. I like magenta here as indicating “danger” more than blue. But there would also be nothing wrong with blue, in terms of visibility
May 21, 2025 at 8:09 PM
I think there’s a good degree of personal preference and subjectivity here. I like magenta here as indicating “danger” more than blue. But there would also be nothing wrong with blue, in terms of visibility
please accept this PR
```
:root {
--bgColor-danger-emphasis: magenta !important;
--fgColor-danger-emphasis: magenta !important;
--bgColor-danger: magenta !important;
--fgColor-danger: magenta !important;
}
```
```
:root {
--bgColor-danger-emphasis: magenta !important;
--fgColor-danger-emphasis: magenta !important;
--bgColor-danger: magenta !important;
--fgColor-danger: magenta !important;
}
```
May 21, 2025 at 7:05 PM
please accept this PR
```
:root {
--bgColor-danger-emphasis: magenta !important;
--fgColor-danger-emphasis: magenta !important;
--bgColor-danger: magenta !important;
--fgColor-danger: magenta !important;
}
```
```
:root {
--bgColor-danger-emphasis: magenta !important;
--fgColor-danger-emphasis: magenta !important;
--bgColor-danger: magenta !important;
--fgColor-danger: magenta !important;
}
```
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!
Ah! Were we lucky enough to entice @pawamoy.bsky.social to Bluesky? :)
February 6, 2025 at 2:02 AM
Ah! Were we lucky enough to entice @pawamoy.bsky.social to Bluesky? :)
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