meghalithic / deepbryo_micro Goto Github PK
View Code? Open in Web Editor NEWThis project forked from agporto/deepbryo
A web app for AI-assisted segmentation of cheilostome bryozoan colonies
License: Other
This project forked from agporto/deepbryo
A web app for AI-assisted segmentation of cheilostome bryozoan colonies
License: Other
following error:
NameError: name 'json' is not defined
Traceback:
File "/home/voje-lab/miniconda3/envs/deepbryo/lib/python3.7/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 552, in _run_script
exec(code, module.__dict__)
File "/home/voje-lab/Documents/GitHub/bryozoa/DeepBryo_micro/app/app.py", line 436, in <module>
main()
File "/home/voje-lab/Documents/GitHub/bryozoa/DeepBryo_micro/app/app.py", line 414, in main
uploaded_img.name,
File "/home/voje-lab/Documents/GitHub/bryozoa/DeepBryo_micro/app/app.py", line 209, in summarize
) = mask_stats(masks[num][idx])
File "/home/voje-lab/Documents/GitHub/bryozoa/DeepBryo_micro/app/app.py", line 160, in mask_stats
cnt_json = json.dumps(cnt_list)
python app/app-cli.py -i ~/Desktop/microporella-jpg/IMAGE -o ~/Documents/GitHub/bryozoa/DeepBryo_micro -p [left, top, right, bottom]
python app/app-cli.py -i ~/Desktop/microporella-jpg/IMAGE -o ~/Documents/GitHub/bryozoa/DeepBryo_micro -sc SCALE
Turned all images from "keep" folders to the optimal orientation for processing
Sorted all images into folders according to orientation of scalebar for all four species. Subfolder names are in the following pattern: "M.intermedia-scalebar-left", located within their respective species folders (eg. ~/Desktop/microporella-subset-jpg/M_intermedia/M.intermedia-scalebar-left).
Finished lists of all images where other species are present (and detected by DeepBryo), for M. discors, M. agonistes and M. speculum. These are named "Speculum_images_with_other_species.csv" etc, located in ~/Documents/GitHub/bryozoa/microporella/Data.
In each file, column 1 is image_id. Column two is blank when image has another bryozoa species detected by DeepBryo. If the presence of other bryozoa species were not immediately obvious to the viewer I have used column two to note their position, eg. "Other species upper left". I also used column two to note images with cracks that affect measurements, or when DeepBryo detects non-bryozoa taxa as zooids with features.
Started list of images with other species present for M. intermedia. Finished images in "M.intermedia-scalebar-left"
To do:
Finished list of all M. intermedia images with other species present.
CLI-csv files are still present in the M.intermedia subfolders, and should be deleted or moved
Manually done csvs moved to their correct place on GitHub (~/Documents/GitHub/bryozoa/microporella/Data/Manual-outputs/M.intermedia)
Redo high throughput with ext version of CLI
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.