Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecular and Cellular Bioengineering (CMCB) / University of Technology, TU Dresden
License: Creative Commons Attribution 4.0 International
Dear Robert,
I tried to create the environment listed here: https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html, however I did not use mambaforge but tried using base conda with this code:
conda create -n biapol devbio-napari python=3.9 pyqt -c conda-forge
However, there seems to be an issue with solving the environment, here is the current terminal session:
Collecting package metadata (current_repodata.json): - DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
\ DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
/ DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/current_repodata.json HTTP/1.1" 304 0
- DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/osx-64/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/osx-64/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /pytorch/noarch/current_repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /pytorch/osx-64/current_repodata.json HTTP/1.1" 200 None
done
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): / DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/osx-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/osx-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /pytorch/osx-64/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0
\ DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /pytorch/noarch/repodata.json HTTP/1.1" 200 None
| WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
/ WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
done
Solving environment: -
It is stuck at solving environemnt since over 1h. Is this issue caused by me not using mambaforge? Or is it a problem with downloading the packages/repodata?
I don't want to use mambaforge and conda simultaneously, as this caused a problem in my base environment path, as mamba edited it.
Thanks for your help in advance,
Best Lukas
look at this in this part of the notebook:
## Applying the algorithm
Voronoi-Otsu-labeling is a **command in clesperanto**, which asks for two sigma parameters. The first sigma controls how close detected cells can be (`spot_sigma`) and second controls how precise segmented objects are outlined (`outline_sigma`). This is the algorithm implemented in the [napari-segment-blobs-and-things-with-membranes](https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes):First you state it is a command in clesperanto, then you use napari-segment-blobs-and-things-with-membranes instead. This is a bit confusing. Probably you could just change the command in clesperanto to command in napari-segment-blobs-and-things-with-membranes
On slides 5 - 18 and 23-24 of Python_data_structures.pdf, there is a 9-element list ("A" - "I") as an example for indexing:
I recommend to remove the index number 9:
Hi,
in /05_feature_extraction/02_sphericity_and_solidity we have the followng code block:
mesh_gastruloid = vedo.load('data/gastruloid.ply')
napari_mesh_gastruloid = nppas.to_napari_surface_data(mesh_gastruloid)
napari_mesh_gastruloid
When running this, I get the following Error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
File ~/anaconda3/envs/biapol2/lib/python3.9/site-packages/IPython/core/formatters.py:344, in BaseFormatter.__call__(self, obj)
342 method = get_real_method(obj, self.print_method)
343 if method is not None:
--> 344 return method()
345 return None
346 else:
File ~/anaconda3/envs/biapol2/lib/python3.9/site-packages/napari_process_points_and_surfaces/_vedo.py:70, in SurfaceTuple._repr_html_(self)
68 bounds = "<br/>".join(["{min_x:.3f}...{max_x:.3f}".format(min_x=min_x, max_x=max_x) for min_x, max_x in zip(mesh.bounds()[::2], mesh.bounds()[1::2])])
69 average_size = "{size:.3f}".format(size=mesh.average_size())
---> 70 center_of_mass = ",".join(["{size:.3f}".format(size=x) for x in mesh.centerOfMass()])
71 scale = ",".join(["{size:.3f}".format(size=x) for x in mesh.scale()])
72 histogram = ""
AttributeError: 'Mesh' object has no attribute 'centerOfMass'
I am using nppas ==0.5.0. and Python==3.9.18
I suspect that in 'centerOfMass'` We have a ZERO instead of a "O".
Thanks for any help!
Dear BIAPol-Team,
first of all many thanks for offering this incredible resource. As an external self-learner, i wanted to ask if there is there a way to get the solutions to the exercises in the jupyter notebook files?
Best,
Lukas
there is a typo on slide 11 of https://github.com/BiAPoL/Bio-image_Analysis_with_Python/blob/main/04_image_segmentation/Image_segmentation.pdf:
The watershed algorithm for binary images allows cutting one object into tow where it’s reasonable.
On slide 15/18 of the descriptive statistics lecture from block 8, I believe that the left side of the equation for the calculation of variance is incorrect. I know this isn't a huge issue, but I wanted to point it out!
On another note, I want to thank the group for making these lectures available. This is a highly valuable resource that I've found real benefit from and have enjoyed using!
I noticed that many students during the class are a little confused about git and github and they struggled and asked questions about how to use the course's repository, where to find the pdfs, jupyter notebooks etc. very frequently.
A brief git tutorial (like the one on conda installation and usage) might be enlightening for the students. This will not only be useful for the course but git and github are amazing tools for students, especially if they start programming for bio-imaging, bioinformatics/statistics, computational biology projects. The tutorial could be done either in the very beginning with the conda installation and focus on version control or it could be done right after the python basics.
Did anyone found a solution to our problem using Napari on Mac?
After installing Napari and using this code:
import napari
viewer = napari.Viewer()
viewer.add_image(image)
labels = viewer.add_labels(binary_image)
...the Error-Message was:
"RuntimeError: Could not load OpenGL library, gl cannot be used"
The images are stored in the same folder as the markdown file and not in an "images" directory
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