JaneliaSciComp/multifish
EASI-FISH analysis pipeline for spatial transcriptomics
Jupyter NotebookBSD-3-Clause
Issues
- 0
Run Bigstream2 in Pipeline
#48 opened by anaste123 - 0
- 1
Run "warp_spots" only produced nothing
#44 opened by FangmingXie - 0
- 2
Make RS-FISH default
#45 opened by krokicki - 4
Skip steps within Stitching
#42 opened by FangmingXie - 3
Add RS-FISH parameters for multiple channels
#20 opened by neugun - 1
Generate MVL from CZI if missing
#41 opened by krokicki - 9
error - registration:moving spots
#29 opened by FangmingXie - 4
Integrate BigStream2
#38 opened by krokicki - 10
- 2
Poor registration result
#37 opened by JienaL - 3
- 3
Error stitching large sample
#43 opened by FangmingXie - 12
Registration glitch in s3 resolution
#40 opened by FangmingXie - 2
Memory calculation
#36 opened by FangmingXie - 0
Add distributed CellPose segmentation
#39 opened by krokicki - 0
adding ROI and spot extraction in the pipeline
#13 opened by limingtan - 1
Other data formats as input.
#25 opened by kenjp1223 - 6
Segmentation_memory for large sample
#35 opened by FangmingXie - 5
Glitch in measure_intensity
#34 opened by FangmingXie - 2
Issue stitching demo_small
#33 opened by FangmingXie - 4
demo_tiny: failed to pull singularity image
#31 opened by FangmingXie - 10
demo_tiny with RS-FISH
#28 opened by FangmingXie - 7
demo_tiny issue on AWS Fsx
#27 opened by FangmingXie - 7
demo_tiny issue on AWS
#26 opened by FangmingXie - 2
- 4
demo_small.sh numpy error
#22 opened by erkinacar5 - 3
Cannot do warp_spots:apply_transform separately
#21 opened by neugun - 7
- 6
Error at registration:moving_spots
#5 opened by bradleycolquitt - 1
Hi ,I am testing this pipeline and would like you to provide some examples. I hope to get your help. I would really appreciate your support and help.
#19 opened by liyongxin123 - 2
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: no descriptor found for reference...
#6 opened by tm1101101 - 5
- 5
Unknown method invocation
#17 opened by erkinacar5 - 0
Automatically adjust segmentation model dir
#16 opened by krokicki - 0
Add segmentation_channels
#15 opened by krokicki - 0
Delete shared_data_dir contents after publish
#12 opened by krokicki - 1
Copy export.n5 to publish_dir
#11 opened by krokicki - 5
- 1
model.predict_instances error
#10 opened by KMSmichelle - 3
Support for dax file input format
#7 opened by pranathivemuri - 9
Spark master process dies
#4 opened by tm1101101 - 4
parseCZITiles error with large CZI
#3 opened by bradleycolquitt - 13
Error with warp_spots on SGE
#2 opened by bradleycolquitt - 1