Because in the second image, the regions that are marked with red seem to be the darker regions that are separated by the slightly brighter boundaries.
However, you said you stained the cells which usually means that they should be the brightest things. @RichardKino_twitter
@halirutan I am trying to measure the endosperm cells which as you mention are the darker regions separated by the slightly brighter boundaries. These cell walls contain small amounts of mixed linkage glycans and arabinoxylan which don't stain brightly but this stain has a quick application and allows for the overall cell morphology to be viewed. The threshold tool on image J is also quite good at removing other intracellular bodies that I don't want
@halirutan Thanks for the advice, that's a good point! I will edit the post and also try to attach and upload the original image.
@halirutan Well based on the scale bar the scale is 0.4775 pixels/um . Therefore for an example area measurement of 10000 which we could assume to be pixels I multiplying this value by the scale factor (10000 x 0.4775 = 4775 um (squared) which is still far too big. Unless I would then need to square root this value?
When I understood you correctly then you need to make 0.47750.4775 to get the area of one pixel. Then you can do 100000.22800625` = 2280 um^2.
Gitter channel is not visible from there.
@RichardKino_twitter I understand. I am glad you got some help. It is OK to post here with a link to a forum thread, to help bump it. I just think it is unfortunate when conversations get split across media because then it is hard to follow it later. The forum also lets people follow individual threads, whereas this channel is one big feed.
so was working on a few other things today and a few students complained about mixing jupyter and imagej. So we made a binder-friendly scijava kernel, so you can start ImageJ notebooks online with a single click, but mayb someone already did this https://mybinder.org/v2/gh/4QuantOSS/scijava-jupyter-kernel/master?filepath=notebooks%2FImageJ.ipynb
@ctrueden you can do all of your presentations in ImageJ directly using Jupyter, reveal.js, RISE, scijava-jupyter-kernel (http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2018/master?filepath=Lectures/01-Introduction.ipynb)
@kmader indeed you'll find that @ctrueden setup binder (https://mybinder.org/v2/gh/imagej/tutorials/master) and somewhere had some RISE stuff floating around
i'm still curious about a version of the scijava-jupyter-kernel that uses a minimal set of dependencies, there is( or maybe was at this point? ) an issue with clashing dependencies when you start importing things like imagej-ops that are directly linked into the kernel which makes it more or less not possible to run any of my code in them at the moment
Do you want me to update it?
Minimal SJJK with scijava grab still not available. Still planned. But right now we are focusing on calling ij from Python via pyjnius. See https://github.com/CellProfiler/notebooks
I guess that doesn't give you clojure though :-(
If we make the system classpath customizable somehow it could alleviate some of the grab difficulties for now.
yes, if i can get 1 or 2 jars on the classpath then my problems pretty much go away
i had another hacked solution that worked without using grab
via the pomegranate library that we use for dependency fetching in clojure land
it isn't pressing right now, as it will be a big leap to switch to RISE-based presentations/demos
(for me)
@kmader If something is missing from github.com/imagej/tutorials to make it more binder friendly, a PR would be appreciated!
getting http://www.imagejfx.net/ as a one-click launch / binder project seems like it would be pretty useful as well
@ctrueden ah shame, it always looked very cool, are there any working projects for ImageJ web-frontends? the binder appmode lets you have interactive notebooks with javascript widgets. It would be a cool way for packaging specific analyses or macros as web-based tools (in this example we took nvidia's latest style transfer and turned it into a little app, https://mybinder.org/v2/gh/4QuantOSS/FastPhotoStyle/master?urlpath=%2Fapps%2Fnotebooks%2Fdemo_app.ipynb)
:point_up: 23. Februar 2018 20:23
the main thing would be tagging it on github as binder-ready
@kmader what do you mean by "tagging it as binder-ready"? The "launch binder" badge was added in December with imagej/tutorials@6ea704a
Is there something else missing?
@kmader @ctrueden alright, I added the
Thanks for the pointer!
binder-ready as a topic to https://github.com/imagej/tutorialsThanks for the pointer!