fish-quant/big-fish

Issues

• Issue extracting cell information

  #91 opened a year ago by Boehmin
  0

• issue loading pretrained model for unet segmentation

  #90 opened a year ago by Boehmin
  0

• spot detection sometimes lead to RuntimeWarning error

  #89 opened a year ago by Amandahsr
  1

• Implementing new spot detection techniques

  #88 opened a year ago by Henley13
  1

• segmentation fault using U-net based model for nuclear segmentation

  #87 opened a year ago by irelamb
  0

• tesorflow-addons dependency

  #86 opened a year ago by irelamb
  0

• Build a docker image

  #85 opened a year ago by Henley13
  0

• Switch entirely from setup.py to pyproject.toml

  #84 opened a year ago by Henley13
  0

• ModuleNotFoundError on installation

  #82 opened 2 years ago by binyaminZ
  3

• FISH spot intensity analysis

  #65 opened a year ago by zwdiscover
  15

• 3D segmentation

  #81 opened a year ago by valerialat
  3

• Display cell id on the segmentation plot

  #76 opened 2 years ago by Henley13
  0

• Threshold setting does not target elbow in plot

  #74 opened 2 years ago by heike-s
  3

• How to use 3d Array Image in BigFish

  #79 opened 2 years ago by ahratul
  2

• BIG-FISH or FISH-quant v2?

  #80 opened 2 years ago by luisub
  2

• U-net based model for nucleus segmentation not working

  #78 opened 2 years ago by zwdiscover
  1

• Getting started on RNAScope analysis

  #75 opened 2 years ago by rahmas36
  10

• Update installation to python 3.9

  #77 opened 2 years ago by ewallace
  1

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

  #72 opened 3 years ago by buttf7
  1

• Cell Segmentation - Cell Information Extraction

  #73 opened 2 years ago by buttf7
  3

• Jupyter Notebook Tutorials won't launch

  #71 opened 3 years ago by rahedges
  2

• v.0.6.1 thresholding type error

  #67 opened 3 years ago by owigg
  8

• Clarify external and internal cell coordinates

  #68 opened 3 years ago by Henley13
  0

• Failed Segmentation

  #63 opened 3 years ago by IrisWEI-1996
  4

• Fail to import multistack module

  #66 opened 3 years ago by zwdiscover
  11

• summarize_extraction_results: add option to specify delimiter

  #50 opened 3 years ago by muellerflorian
  0

• read_array_from_csv: add option to specify headers

  #51 opened 3 years ago by muellerflorian
  0

• Stop pinning requirements in setup.py, use test to check compatybility

  #57 opened 3 years ago by Czaki
  5

• read_array_from_csv: allow header rows

  #33 opened 3 years ago by muellerflorian
  1

• Plot elbow, return threshold`

  #56 opened 3 years ago by SachinDavis
  1

• Set spot detection threshold based on signal:background

  #46 opened 4 years ago by jstitlow
  1

• Increase speed of spot detection

  #44 opened 4 years ago by jstitlow
  1

• Manual Cell Segmentation

  #58 opened 3 years ago by charliemoffatt
  4

• Changing the colour on plots

  #54 opened 3 years ago by SachinDavis
  2

• Remove super-expressing cells from analysis?

  #45 opened 3 years ago by jstitlow
  2

• Different thresholding for nuclei and cytoplasm

  #48 opened 3 years ago by zhenzuo2
  1

• decompose_cluster() inserting large number of invisible RNAs at edge of image

  #42 opened 3 years ago by marykthompson
  1

• Calculating the PSF_X, PSF_Z values

  #55 opened 3 years ago by SachinDavis
  1

• Sharpness measure goes below 1

  #64 opened 3 years ago by michimiura
  1

• Pandas version

  #59 opened 3 years ago by luisub
  2

• Allow coordinates in float for cell extraction functions

  #37 opened 3 years ago by Henley13
  0

• Rename function for cluster decomposition and foci detection

  #38 opened 3 years ago by Henley13
  0

• SNR calculation is very slow with many spots and larger images

  #40 opened 3 years ago by muellerflorian
  2

• Add a sphinx documentation

  #31 opened 3 years ago by Henley13
  0

• Add plot spot-threshold

  #32 opened 3 years ago by Henley13
  0

• Cell segmentation in 3-dimensions?

  #47 opened 4 years ago by SachinDavis
  2

• plot.utilities.saveplot() not writing image

  #43 opened 4 years ago by jstitlow
  2

• Estimating # of spots in a cluster

  #41 opened 4 years ago by jstitlow
  6

• Effective error message when no spots are (pre) detected

  #39 opened 4 years ago by bellonet
  4

• Add SNR functions

  #34 opened 4 years ago by Henley13
  1