Owner

dchaley

4 indexed repositories · View on GitHub

deepcell-segmentation
Tools & guidance to scale DeepCell segmentation on Google Cloud Batch

Jupyter Notebook · 9 stars
qupath-project-initializer
Tools to initialize a QuPath project from input files

Kotlin · 1 star
rc
Config files, etc

Vim Script · 1 star
you-need-a-splitter
Split transactions on YNAB + send to Splitwise.

Kotlin · 0 stars

Open All

48 open issues indexed

What to do with QuPath image paths? Open

dchaley/qupath-project-initializer#5 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Faster builds with tool: jib ? Open

dchaley/qupath-project-initializer#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create ramdisk to store working files Open

question

dchaley/qupath-project-initializer#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CVE-2024-36114 in airlift/aircompressor (high) Open

vuln

dchaley/qupath-project-initializer#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CVE-2023-32697 in xerial/sqlite-jdbc (high) Open

vuln

dchaley/qupath-project-initializer#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
CVE-2023-6378 in logback (high) Open

vuln

dchaley/qupath-project-initializer#27 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handle errors on upload/download failure Open

dchaley/qupath-project-initializer#33 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Determine disk sizing needs Open

dchaley/qupath-project-initializer#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Set up cache for multistage build Open

build / test / ship

dchaley/qupath-project-initializer#54 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Import GeoJSON files Open

dchaley/qupath-project-initializer#56 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ClassCastException when YNAB_ACCESS_TOKEN missing Open

bug

dchaley/you-need-a-splitter#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add loading state for modifying a transaction Open

dchaley/you-need-a-splitter#13 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Bad layout at smaller screen size Open

dchaley/you-need-a-splitter#29 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Batch requests to YNAB API Open

dchaley/you-need-a-splitter#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Document what the mesmer sample data files are Open

documentation good first issue

dchaley/deepcell-segmentation#25 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Rename Data Folder to VanValen Open

documentation good first issue

dchaley/deepcell-segmentation#51 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Generate sample images for 10x genomics file: human-prostate-cancer-20210727-725mb Open

documentation

dchaley/deepcell-segmentation#84 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Investigate: post-processing performance: fill_holes Open

performance

dchaley/deepcell-segmentation#85 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Investigate: post-processing performance: watershed Open

performance

dchaley/deepcell-segmentation#86 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Merge PR to scikit-image Open

dchaley/deepcell-segmentation#97 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Integrate fast-hybrid into scikit Open

dchaley/deepcell-segmentation#130 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Has benchmarking moved to BigQuery? Open

dchaley/deepcell-segmentation#200 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Investigate container streaming Open

performance

dchaley/deepcell-segmentation#204 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Container size optimization Open

enhancement performance

dchaley/deepcell-segmentation#209 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Investigate cloud build caching Open

build / test / ship

dchaley/deepcell-segmentation#225 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Figure out model_zoo fix [arm64] Open

bug

dchaley/deepcell-segmentation#232 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Consider including TF model on Docker container Open

dchaley/deepcell-segmentation#273 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add a Teams-formatted webhook call on pipeline success Open

dchaley/deepcell-segmentation#283 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add user-project parameters to storage API calls Open

dchaley/deepcell-segmentation#297 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
VULNs: Can we update TF? Open

help wanted vuln

dchaley/deepcell-segmentation#308 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update README to share batch benchmark results Open

dchaley/deepcell-segmentation#310 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Don't create segment job gather-benchmark tasks if the BigQuery table is blank Open

good first issue performance

dchaley/deepcell-segmentation#313 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Scale preprocessing Open

dchaley/deepcell-segmentation#320 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Scale prediction Open

dchaley/deepcell-segmentation#321 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Scale postprocessing Open

dchaley/deepcell-segmentation#322 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update benchmarking to include total time Open

dchaley/deepcell-segmentation#345 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve deep_watershed memory usage Open

dchaley/deepcell-segmentation#359 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Allow working directory reuse Open

dchaley/deepcell-segmentation#375 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix package discovery for deepcell_imaging subpackages Open

dchaley/deepcell-segmentation#381 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Need to squeeze after selecting prediction channel for multi-compartment predictions Open

dchaley/deepcell-segmentation#388 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Split compartment postprocessing into separate tasks Open

dchaley/deepcell-segmentation#389 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
PRs should have action that runs pytest Open

build / test / ship

dchaley/deepcell-segmentation#399 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix python in container Open

dchaley/deepcell-segmentation#408 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Only install tensorflow into container Open

dchaley/deepcell-segmentation#409 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Vim typescript syntax highlighting is broken Open

bug

dchaley/rc#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handle dark-notify dependency for mac Open

dchaley/rc#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Build qupath launcher Open

dchaley/deepcell-segmentation#410 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Convert to gbatchkit Open

dchaley/deepcell-segmentation#413 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026

dchaley

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