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View Code? Open in Web Editor NEWGuides for using OMERO
Home Page: https://omero-guides.readthedocs.io
License: BSD 2-Clause "Simplified" License
Guides for using OMERO
Home Page: https://omero-guides.readthedocs.io
License: BSD 2-Clause "Simplified" License
Hi @jburel et al,
I was just collecting information about licenses of training materials and here in this repository I was a little bit confused. In the github repository exists a BSD 2 license file but on the bottom of the rendered page it says:
Would it be possible to show the right license in the rendered website? That way it would be easier to Reuse the materials following the FAIR principles.
Thanks!
best,
Robert
include in the index page link to the videos we have on youtube
cc @jburel
Improve instructions at https://omero-guides.readthedocs.io/en/latest/upload/docs/import-cli.html
Regular CLI import (not in-place) should not connect via ssh to the server or use images from /in-place-import/
directory.
The 'connect via ssh' instructions should be moved down since the in-place import section starts with "We are still in the omero server directory:"
See ome/www.openmicroscopy.org#401 (comment)
Create a symlink at the top level of the guides, which would enable to have also a url which says imagej
in it, and which would redirect to the fiji guides.
cc @sbesson
This uses code from https://napari.org/stable/tutorials/segmentation/annotate_segmentation.html
I have tested this workflow with an RGB image from IDR, exported with Batch_Image_Export, but you can also simply save https://idr.openmicroscopy.org/webclient/render_image/179764/0/0/ and import it...
Then, using napari-omero
open it in napari with $ omero napari view Image:ID
Copy the code from the link above - you just need the imports (maybe not all needed) and the segment()
method.
Specifically I copied this code and pasted it into napari terminal...
import numpy as np
from skimage import data
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label, regionprops_table
from skimage.morphology import closing, square, remove_small_objects
import napari
def segment(image):
"""Segment an image using an intensity threshold determined via
Otsu's method.
Parameters
----------
image : np.ndarray
The image to be segmented
Returns
-------
label_image : np.ndarray
The resulting image where each detected object labeled with a unique integer.
"""
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(4))
# remove artifacts connected to image border
cleared = remove_small_objects(clear_border(bw), 20)
# label image regions
label_image = label(cleared)
return label_image
Then you can use the first "Red" layer from the RGB, slice it to 2D (required by code above) and compute()
to turn it from a dask array into a numpy array, which also seems to be needed.
image = viewer.layers[0].data
image.shape
>>> (1, 1, 1024, 1344)
plane = image[0, 0]
plane = plane.compute()
Now we can use the segment()
method we created above to give us labels...
Then we add back 2 dimensions to get back to 4D (shape is (1, 1, 1024, 1344)
again) which seems to be needed for saving to OMERO.
labels = segment(plane)
lab3d = np.expand_dims(labels, axis=0)
lab4d = np.expand_dims(lab3d, axis=0)
Finally, we can add the labels to the viewer to see them in napari
...
viewer.add_labels(lab4d)
Then you can hit Save ROIs to OMERO
and you should see the labels saved as new Masks in OMERO:
Currently splitting the long walkthrough into several documents.
This is currently done as g.doc. The file will then be converted into .rst
files
g.docs are under OME Team > Training > General walkthroughs
The instructions and screenshot don't match the actual script any longer:
https://omero-guides.readthedocs.io/en/latest/fiji/docs/threshold_scripting.html#step-by-step
In one of the earlier steps of the documentation, it says to "Find the main webpage of the OME project". I searched for it on Google and I did find the webpage without much difficulty. However, I think it would be more straightforward if the guide just mentions the name of the website. So it would instead say to "Search for openmicroscopy.org on your web browser".
It's a minor change, but I think it helps being more specific.
.. _Resources:
Resources
---------
Should underscore anchors will need to be renamed per guide.
.. |image16| image:: images/Iviewer16.png
:width: 0.22917in
:height: 0.1875in
16 doesn't exist:
(base) /opt/own-guides/omero-guides $find . -name Iviewer1*.png
./_build/html/_images/Iviewer1.png
./_build/html/_images/Iviewer11.png
./_build/html/_images/Iviewer10.png
./_build/html/_images/Iviewer12.png
./_build/html/_images/Iviewer13.png
./_build/html/_images/Iviewer14.png
./_build/html/_images/Iviewer1b.png
./_build/html/_images/Iviewer1c.png
./_build/html/_images/Iviewer15.png
./iviewer/docs/images/Iviewer1.png
./iviewer/docs/images/Iviewer11.png
./iviewer/docs/images/Iviewer10.png
./iviewer/docs/images/Iviewer12.png
./iviewer/docs/images/Iviewer13.png
./iviewer/docs/images/Iviewer14.png
./iviewer/docs/images/Iviewer1b.png
./iviewer/docs/images/Iviewer1c.png
./iviewer/docs/images/Iviewer15.png
-**Setup:**
-----------
+Setup
+-----
This text has been changed.
Migrated from #54
I was looking at a couple of guides, and I noticed that some of them show example images wherein an outreach account is used as a placeholder for the user's account. This seemed pretty confusing to me, as I'd wrongly assumed at first that I needed to use the server address shown in the image and not my own. I feel like this could've been better explained in the guide itself. I've only looked at two guides so far, so I'm not too sure if this is just an issue with the guides I've looked at, or if it extends to other guides as well.
Here are links to the guides I've looked at:
Crop and Import Image is on Step 4
Import Data using the Desktop Client
Image is on Step 2
I've been using an outreach account to work on my internship, and I had noticed that a lot of the data used in the guides as reference were not present in the account I was using. This confused me at first, but then I noticed in the example images that the user account being used was 'trainer-1 trainer-1' from the 'Lab1' group. I switched to this user account had all the data I had needed and I proceeded as normal. Because of this confusion, I think it should be specified in the guide as to which account should be used during training, as some accounts don't seem to have all the data used in the guides.
On steps 12 and 13 of the documentation, it encourages finding YouTube videos about OMERO features, and specifically about OMERO.figure and OMERO.parade. While the YouTube videos were helpful, I think it would also help if the documentation suggested using the OMERO-guides website too. It has helped me a lot in understanding not just these specific steps, but a lot of the other steps in the documentation as well.
When trying to move all from to this repo, it seems that the missing chapters in the guides here (which are present in help) are
After the recent post on image.sc about OMERO training guides from the I3D:bio project, I discussed with @Tom-TBT @SchmChris @sukunis et al. about referencing the resources from omero-guides (or other OME documentation locations). This issue collects potential paths forward for that integration.
Shares have been deprecated but not really replaced by anything in the web client
It has been mentioned several times during workshops or discussion on forum see for example https://forum.image.sc/t/omero-sharing-data-with-users-you-are-not-in-a-group-with/48520/3
The closest we have is the "omero-cli-duplicate" plugin. An entry in the guide will be useful to have
cc @joshmoore @pwalczysko
this should become a guide on how to link 3rd
This is not only "BF" or omero only it is more "ome-guide", we need to write out to deploy, run such
We could rename omero-guides to ome-guides
if we opt for a change of name, we will need to check the implication on readthedocs
cc @sbesson @joshmoore @olatarkowska
Fix the build problems https://readthedocs.org/projects/omero-guides/builds/15222671/ - build is failing, probably because of the Sphinx version issues.
cc @jburel
It is a good feature to be able to click on the top-left-corner Docs
link which brings you to https://omero-guides.readthedocs.io/en/latest/index.html
This feature works also when you are in a deeper level, such as https://omero-guides.readthedocs.io/en/latest/upload/docs/import-desktop-client.html
But if you navigate to such deeper level using Search, such as
ilastik
brings no resultsDesign issue with the goal to come up with a walkthrough for an external (non-OME-Team) scientist(s)/facility, which should help them to set up a training on OMERO on their site, but without direct participation of the trainers from OME Team.
Please see attached pdf
2021-04-14-training-walkthrough.pdf
for the item-by-item walkthrough - this design issue is a work in progress, and new pdfs will come as we are going further with the prep of this walkthrough.
The outline of the walkthrough points:
LIST OF VERSIONS of DETAILED WALKTHROUGH (to be expanded as new content comes)
Include a link from an omero-guide to tips and tricks posted on image.sc
cc @jburel
See @joshmoore comment on #54 (comment)
(Eventually I could imagine having some icons or maybe a workflow graphic at the top of the page.)
cc @joshmoore
Hello, I tried to use the script to analyse figures on omero with cellprofiler using the pythonAPI. However, it is written that the pipleine accept only images with 2 channels, but my images have 4. Do you know if there is a possibility to use my cellprofiler pipeline on omero even if my images have more than 2 chanels ? When i use my pipeline normally (on cellprofiler directly) it works well i just need to separate the chanels (and my images are in 3D). How can i modifiy the script to do it ?
When looking for a chapter such as upload metadata (import metadata using CLI). Starting from a top level menu, click on General Concenpts and there I can click on Import. But this will not bring me to upload metadata - from there, I have to know that I have to go one-up in the top-level menu to Upload. From Upload I can click onto upload metadata.
Suggestion: Add the Upload item as a clickable link on General Concenpts page.
Edit:
I will leave this open for capturing
Eventually I could imagine having some icons or maybe a workflow graphic at the top of the page.)
follow-up from the #54 (comment)
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