fish-quant/big-fish issues and pull requests

#93 - Problem with BigFish Array Indexing

Issue - State: open - Opened by LR-MVU about 1 month ago

#92 - [Big Fish] Fixed issue with deprecated package.

Pull Request - State: open - Opened by CPBach about 1 year ago - 1 comment

#91 - Issue extracting cell information

Issue - State: open - Opened by Boehmin about 1 year ago

#90 - issue loading pretrained model for unet segmentation

Issue - State: open - Opened by Boehmin about 1 year ago

#89 - spot detection sometimes lead to RuntimeWarning error

Issue - State: closed - Opened by Amandahsr over 1 year ago - 1 comment

#88 - Implementing new spot detection techniques

Issue - State: open - Opened by Henley13 over 1 year ago - 1 comment
Labels: enhancement, new features

#87 - segmentation fault using U-net based model for nuclear segmentation

Issue - State: open - Opened by irelamb over 1 year ago

#86 - tesorflow-addons dependency

Issue - State: open - Opened by irelamb over 1 year ago

#85 - Build a docker image

Issue - State: open - Opened by Henley13 over 1 year ago
Labels: packaging

#84 - Switch entirely from setup.py to pyproject.toml

Issue - State: open - Opened by Henley13 over 1 year ago
Labels: packaging

#83 - v0.6.3

Pull Request - State: open - Opened by Henley13 over 1 year ago

#82 - ModuleNotFoundError on installation

Issue - State: open - Opened by binyaminZ over 1 year ago - 3 comments

#81 - 3D segmentation

Issue - State: closed - Opened by valerialat almost 2 years ago - 3 comments

#80 - BIG-FISH or FISH-quant v2?

Issue - State: closed - Opened by luisub almost 2 years ago - 2 comments

#79 - How to use 3d Array Image in BigFish

Issue - State: closed - Opened by ahratul about 2 years ago - 2 comments

#78 - U-net based model for nucleus segmentation not working

Issue - State: closed - Opened by zwdiscover about 2 years ago - 1 comment

#77 - Update installation to python 3.9

Issue - State: closed - Opened by ewallace about 2 years ago - 1 comment

#76 - Display cell id on the segmentation plot

Issue - State: closed - Opened by Henley13 over 2 years ago
Labels: new features

#75 - Getting started on RNAScope analysis

Issue - State: closed - Opened by rahmas36 over 2 years ago - 10 comments

#74 - Threshold setting does not target elbow in plot

Issue - State: closed - Opened by heike-s over 2 years ago - 3 comments

#73 - Cell Segmentation - Cell Information Extraction

Issue - State: closed - Opened by buttf7 over 2 years ago - 3 comments

#72 - Is there a way outside of visual inspection to set threshold value for watershed segementation?

Issue - State: open - Opened by buttf7 over 2 years ago - 1 comment
Labels: stale

#71 - Jupyter Notebook Tutorials won't launch

Issue - State: closed - Opened by rahedges over 2 years ago - 2 comments

#70 - v0.6.2

Pull Request - State: closed - Opened by Henley13 over 2 years ago

#69 - allow int 32-bit as input for numerous functions + minor refactoring

Pull Request - State: closed - Opened by Henley13 over 2 years ago

#68 - Clarify external and internal cell coordinates

Issue - State: open - Opened by Henley13 over 2 years ago
Labels: enhancement

#67 - v.0.6.1 thresholding type error

Issue - State: closed - Opened by owigg over 2 years ago - 8 comments

#66 - Fail to import multistack module

Issue - State: closed - Opened by zwdiscover almost 3 years ago - 11 comments

#65 - FISH spot intensity analysis

Issue - State: closed - Opened by zwdiscover almost 3 years ago - 15 comments

#64 - Sharpness measure goes below 1

Issue - State: closed - Opened by michimiura almost 3 years ago - 1 comment

#63 - Failed Segmentation

Issue - State: closed - Opened by IrisWEI-1996 almost 3 years ago - 4 comments

#62 - v0.6.1

Pull Request - State: closed - Opened by Henley13 almost 3 years ago

#61 - v0.6.0

Pull Request - State: closed - Opened by Henley13 almost 3 years ago

#60 - Multistack subpackage

Pull Request - State: closed - Opened by Henley13 almost 3 years ago

#59 - Pandas version

Issue - State: closed - Opened by luisub about 3 years ago - 2 comments

#58 - Manual Cell Segmentation

Issue - State: closed - Opened by charliemoffatt about 3 years ago - 4 comments
Labels: enhancement, new features

#57 - Stop pinning requirements in setup.py, use test to check compatybility

Issue - State: closed - Opened by Czaki about 3 years ago - 5 comments

#56 - Plot elbow, return threshold`

Issue - State: open - Opened by SachinDavis over 3 years ago - 1 comment
Labels: stale

#55 - Calculating the PSF_X, PSF_Z values

Issue - State: closed - Opened by SachinDavis over 3 years ago - 1 comment

#54 - Changing the colour on plots

Issue - State: closed - Opened by SachinDavis over 3 years ago - 2 comments

#53 - v0.5.0 (hotfix)

Pull Request - State: closed - Opened by Henley13 over 3 years ago

#52 - Documentation sphinx

Pull Request - State: closed - Opened by Henley13 over 3 years ago

#51 - read_array_from_csv: add option to specify headers

Issue - State: closed - Opened by muellerflorian over 3 years ago
Labels: enhancement, good first issue

#50 - summarize_extraction_results: add option to specify delimiter

Issue - State: closed - Opened by muellerflorian over 3 years ago
Labels: enhancement, good first issue

#49 - Features/unet

Pull Request - State: closed - Opened by Henley13 over 3 years ago

#48 - Different thresholding for nuclei and cytoplasm

Issue - State: closed - Opened by zhenzuo2 over 3 years ago - 1 comment

#47 - Cell segmentation in 3-dimensions?

Issue - State: closed - Opened by SachinDavis over 3 years ago - 2 comments

#46 - Set spot detection threshold based on signal:background

Issue - State: open - Opened by jstitlow over 3 years ago - 1 comment
Labels: stale

#45 - Remove super-expressing cells from analysis?

Issue - State: closed - Opened by jstitlow over 3 years ago - 2 comments

#44 - Increase speed of spot detection

Issue - State: open - Opened by jstitlow over 3 years ago - 1 comment
Labels: stale

#43 - plot.utilities.saveplot() not writing image

Issue - State: closed - Opened by jstitlow over 3 years ago - 2 comments

#42 - decompose_cluster() inserting large number of invisible RNAs at edge of image

Issue - State: closed - Opened by marykthompson almost 4 years ago - 1 comment

#41 - Estimating # of spots in a cluster

Issue - State: closed - Opened by jstitlow almost 4 years ago - 6 comments

#40 - SNR calculation is very slow with many spots and larger images

Issue - State: closed - Opened by muellerflorian almost 4 years ago - 2 comments
Labels: enhancement

#39 - Effective error message when no spots are (pre) detected

Issue - State: closed - Opened by bellonet almost 4 years ago - 4 comments

#38 - Rename function for cluster decomposition and foci detection

Issue - State: closed - Opened by Henley13 almost 4 years ago
Labels: enhancement

#37 - Allow coordinates in float for cell extraction functions

Issue - State: closed - Opened by Henley13 almost 4 years ago
Labels: enhancement

#36 - v0.5.0

Pull Request - State: closed - Opened by Henley13 about 4 years ago

#35 - Features - spot modeling / SNR / subpixel fitting

Pull Request - State: closed - Opened by Henley13 about 4 years ago

#34 - Add SNR functions

Issue - State: closed - Opened by Henley13 about 4 years ago - 1 comment
Labels: new features

#33 - read_array_from_csv: allow header rows

Issue - State: closed - Opened by muellerflorian about 4 years ago - 1 comment
Labels: enhancement

#32 - Add plot spot-threshold

Issue - State: closed - Opened by Henley13 about 4 years ago
Labels: new features

#31 - Add a sphinx documentation

Issue - State: closed - Opened by Henley13 about 4 years ago
Labels: enhancement, documentation

#30 - Allow subpixel spot detection

Issue - State: closed - Opened by Henley13 about 4 years ago
Labels: new features

#29 - Adapt centrosomal features in 3D

Issue - State: closed - Opened by Henley13 about 4 years ago
Labels: enhancement

#28 - Update README.md

Pull Request - State: closed - Opened by muellerflorian about 4 years ago

#27 - v0.4.0

Pull Request - State: closed - Opened by Henley13 about 4 years ago

#26 - [read_array_from_csv] add more flexibility when reading results

Issue - State: closed - Opened by muellerflorian over 4 years ago - 3 comments
Labels: enhancement

#25 - Integrate travis in the repository

Issue - State: closed - Opened by Henley13 over 4 years ago
Labels: packaging

#24 - Integrate codecov in the repository

Issue - State: closed - Opened by Henley13 over 4 years ago
Labels: packaging

#23 - Refactor bigfish.deep_learning

Issue - State: closed - Opened by Henley13 over 4 years ago
Labels: enhancement

#22 - Add cell label in bigfish.stack.extract_cell

Issue - State: closed - Opened by Henley13 over 4 years ago - 1 comment
Labels: enhancement

#21 - Refactor bigfish.classification

Issue - State: closed - Opened by Henley13 over 4 years ago
Labels: enhancement

#20 - Add parameters in bigfish.detection.decompose_cluster

Issue - State: closed - Opened by Henley13 over 4 years ago
Labels: enhancement

#19 - Replace 'experience' by 'experiment'

Issue - State: closed - Opened by Henley13 over 4 years ago
Labels: documentation

#18 - Function to save a csv file with basic results from bigfish.stack.extract_cell

Issue - State: closed - Opened by Henley13 over 4 years ago - 2 comments
Labels: enhancement

#17 - Need to discriminate object inside the nucleus

Issue - State: closed - Opened by Henley13 over 4 years ago - 2 comments
Labels: enhancement

#16 - [extract_cell] add sub-cellular position of isolated RNAs

Issue - State: closed - Opened by muellerflorian over 4 years ago - 1 comment
Labels: enhancement

#15 - [extract_cell] add identifier of cell label to fov_results

Issue - State: closed - Opened by muellerflorian over 4 years ago - 2 comments
Labels: enhancement