multifish

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## Bug report ## Description of the problem When no spots are detected, Takashi says that the pipeline throws an error. He had to create empty result files to handle...

krokicki

Run Bigstream2 in Pipeline

1

## Bug report Hi, I was trying to do registration of our large image data using Bigsteam2 in EASI-FISH Pipeline, I changed most parameters exposed, including: --bigstream_global_steps --bigstream_local_steps --global_iterations --local_iterations...

anaste123

## Bug report ## Description of the problem Data information： total 16 tiles the dimensions of each tile is [1920,1920,1099] datatype:uint16 the pixel resolution is [0.23,0.23,0.42] sum size of two...

azzhu

Run "warp_spots" only produced nothing

1

## Bug report ## Description of the problem I tried to run `warp_spots` only using `main.nf` by skipping all other steps. The pipeline ran through with no error message, but...

FangmingXie

## Bug report ## Description of the problem Spot extraction fails when running on Janelia's grid with "lsf" profile. (A clear and concise description of the nature of issue.) ##...

cgoina

Make RS-FISH default

2

Currently, only demo_tiny uses RS-FISH. It should be the default for all the demo data sets.

krokicki

Skip steps within Stitching

4

## New feature I was trying to stitch a large sample. The whole stitching pipeline seems to have a few consecutive steps, including: - parse czi tile - czi2n5 -...

FangmingXie

Add RS-FISH parameters for multiple channels

3

Hi Konrad and Cristian, I am wondering if I can use different RS-FISH parameters for spot extraction or can you please add this feature? Please see the following request. ##...

neugun

Generate MVL from CZI if missing

1

If MVL file is missing, it may be possible to create one from the CZI metadata (for the latest CZI formats).

krokicki

Integrate BigStream2

4

Integrate BigStream2 to replace BigStream1 for registration. Compare results and performance.

krokicki