aleks-szczure / thunderfish Goto Github PK
View Code? Open in Web Editor NEWThunderFISH: Script for sparse RNA-FISH data analysis with increased throughput with sample preparation protocol
ThunderFISH: Script for sparse RNA-FISH data analysis with increased throughput with sample preparation protocol
Dear Aleksander,
Thanks a lot for this pipeline.
I was recently trying ThunderFISH pipeline on example data you provided.
However, the pipeline stuck after cell masking as it stated that
There are no images open in line 233 (called from line 247) close ( <)>
Would you mind have a look at this issue please?
I also attached the log below.
Best regards,
Kasit
1/3 Choose folder containing original data stacks (.Tiff) . . .
2/3 Choose output folder for FISH channel . . .
3/3 Choose output folder for MASK channel . . .
. . . PROCESSING . . .
Progress 1/6
1
1
1
Progress 2/6
Progress 3/6
27
25
16
Progress 4/6
4) Now review your single cell masks and delete the ones that you don't like !
Manually remove accidentally merged cells or excessively cut cells !
6
68
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.