nf-core/deepcell/mesmer @ 0.0.0-be790aa
Summary
Deepcell/mesmer segmentation for whole-cell
Get started
Add the following snippet to your workflow script to include this module.
include { DEEPCELL_MESMER } from 'nf-core/deepcell/mesmer'
License
MIT License
Process
Name
|
DEEPCELL_MESMER |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
img
file
|
Multichannel image file *.{tiff,tif,h5,hdf5}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
membrane_img
file
|
Optional membrane image to be provided separately. *.{tiff,tif,h5,hdf5}
|
Output
4 channels
#1
mask
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tif
file
|
File containing the mask. *.{tif, tiff}
|
#2
versions_python
tuple
${task.process}
string
|
The name of the process |
|---|---|
python
string
|
The name of the tool |
python --version | sed 's/Python //'
eval
|
The expression to obtain the version of the tool |
#3
versions_deepcell
tuple
${task.process}
string
|
The name of the process |
|---|---|
deepcell
string
|
The name of the tool |
pip show 'DeepCell' | sed '2!d;s/Version: //'
eval
|
The expression to obtain the version of the tool |
#4
versions_deepcellapplications
tuple
${task.process}
string
|
The name of the process |
|---|---|
deepcell-applications
string
|
The name of the tool |
0.4.1
string
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| mesmer | Deep cell is a collection of tools to segment imaging data | https://github.com/vanvalenlab/deepcell-tf |
| Version | 0.0.0-be790aa |
|---|---|
| Commit ID | be790aafaa178554b403f862164eb27042f0b35a |
| Release Date | 24 Apr 2026 15:00:42 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fdeepcell%2Fmesmer/0.0.0-be790aa/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/deepcell/mesmer/blobs/sha256:4aadc2b57e9dfef5986f1c12c4fd172c3834f4155a03ec0c2f4278606095b9e6 |
| Size | 2.6 KB |
| Checksum | sha256:4aadc2b57e9dfef5986f1c12c4fd172c3834f4155a03ec0c2f4278606095b9e6 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-be790aa | 24 Apr 2026 15:00:42 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:09:57 (UTC) | 3 | 2.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:56:48 (UTC) | 3 | 2.3 KB |