Comments (8)
Hi @Bunmi0616 ,
This is due to an annoying issue that Mac generates hidden .mcd files when creating a ZIP archive. (See #33).
Deleting these hidden .zip files from the archive does fix this issue.
This will be definitely fixed in future versions of this workflow when porting everything to the imctools
version 2 library.
from imcsegmentationpipeline.
This issue is fixed in version 2.0.1
from imcsegmentationpipeline.
from imcsegmentationpipeline.
Hi Bunmi,
Could you please describe what kind of issue it is?
Best regards,
Anton
from imcsegmentationpipeline.
Recently I got IMC data from my partner. He just gave me a .mcd file. Can I use this pipeline under this condition?
from imcsegmentationpipeline.
Hi Anton,
I could not get the the notebook to run even after loading in the imctools environment. Attempting to download imctools using pip install the version 2.0.1 i get an error message about pip dependencies.
After running the pipeline, (without the 3_measure mask in CP) the histocat folder does not contain the masks for the designated files even though I ran the "generate histocat folder with masks" function.
Thanks for your help,
Bunmi
from imcsegmentationpipeline.
Closing under the assumption that this is not relevant anymore. Please reopen if issues persist.
from imcsegmentationpipeline.
from imcsegmentationpipeline.
Related Issues (20)
- Cell segmentation in placental cells. HOT 2
- Error while loading summarizestack HOT 3
- Creating unique .h5 files for Ilastik from ImcSegmentationPipeline Jupyter notebook HOT 2
- Image Stacks Generation - Key Error HOT 19
- Switch use of readimc in pipeline HOT 1
- Error installing conda environment HOT 7
- Pre-processing error HOT 8
- Nd145 not in list error when generating image stacks HOT 5
- Error“Generate image stacks for downstream analyses” HOT 13
- single-cell expression data HOT 1
- Presence of undefined channels during conversion from MCD to ome-TIFF HOT 2
- Numpy float or unsigned integer in TIFF images HOT 3
- Unable to load Ilastik crop pipeline file to CellProfiler HOT 3
- Jupyter-lab did not open Jupyter notebook HOT 5
- TIFF output all black HOT 4
- windows zip file compression type not recognized
- Corrupt MCD file - using .txt instead HOT 4
- Error in 3_measure_mask.cppipe HOT 4
- Error when creating spatial experiment object from IMC segmentation pipeline: 'Could not guess delimiter'. HOT 2
- 1_prepare_ilastik.cppipe pipeline not working HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from imcsegmentationpipeline.