-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'main' of https://github.com/catalystneuro/voluseg-dendr…
…o-app into main
- Loading branch information
Showing
2 changed files
with
211 additions
and
0 deletions.
There are no files selected for viewing
Empty file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,211 @@ | ||
| { | ||
| "name": "voluseg", | ||
| "description": "Voluseg processors", | ||
| "processors": [ | ||
| { | ||
| "name": "voluseg_processor", | ||
| "description": "Run Voluseg for volumetric segmentation.", | ||
| "label": "voluseg_processor", | ||
| "image": "catalystneuro/dendro-voluseg:0.1.0", | ||
| "executable": "/app/main.py", | ||
| "inputs": [ | ||
| { | ||
| "name": "input", | ||
| "description": "Input NWB file in .nwb or .nwb.lindi.tar format" | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "name": "output", | ||
| "description": "Output embedding in .lindi.tar format" | ||
| } | ||
| ], | ||
| "parameters": [ | ||
| { | ||
| "name": "detrending", | ||
| "type": "str", | ||
| "description": "Type of detrending: 'standard', 'robust', or 'none'", | ||
| "defaultValue": "standard", | ||
| "options": [ | ||
| "standard", | ||
| "robust", | ||
| "none" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "registration", | ||
| "type": "str", | ||
| "description": "Quality of registration: 'high', 'medium', 'low' or 'none'", | ||
| "defaultValue": "medium", | ||
| "options": [ | ||
| "high", | ||
| "medium", | ||
| "low", | ||
| "none" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "registration_restrict", | ||
| "type": "str", | ||
| "description": "Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0)", | ||
| "defaultValue": "" | ||
| }, | ||
| { | ||
| "name": "diam_cell", | ||
| "type": "float", | ||
| "description": "Cell diameter in microns", | ||
| "defaultValue": 6.0 | ||
| }, | ||
| { | ||
| "name": "ds", | ||
| "type": "int", | ||
| "description": "Spatial coarse-graining in x-y dimension", | ||
| "defaultValue": 2 | ||
| }, | ||
| { | ||
| "name": "planes_pad", | ||
| "type": "int", | ||
| "description": "Number of planes to pad the volume with for robust registration", | ||
| "defaultValue": 0 | ||
| }, | ||
| { | ||
| "name": "planes_packed", | ||
| "type": "bool", | ||
| "description": "Packed planes in each volume (for single plane imaging with packed planes)", | ||
| "defaultValue": false | ||
| }, | ||
| { | ||
| "name": "parallel_clean", | ||
| "type": "bool", | ||
| "description": "Parallelization of final cleaning (True is fast but memory intensive)", | ||
| "defaultValue": true | ||
| }, | ||
| { | ||
| "name": "parallel_volume", | ||
| "type": "bool", | ||
| "description": "Parallelization of mean-volume computation (True is fast but memory intensive)", | ||
| "defaultValue": true | ||
| }, | ||
| { | ||
| "name": "save_volume", | ||
| "type": "bool", | ||
| "description": "Save registered volumes after segmentation (True keeps a copy of the volumes)", | ||
| "defaultValue": false | ||
| }, | ||
| { | ||
| "name": "type_timepoints", | ||
| "type": "str", | ||
| "description": "Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom'", | ||
| "defaultValue": "dff", | ||
| "options": [ | ||
| "dff", | ||
| "periodic", | ||
| "custom" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "type_mask", | ||
| "type": "str", | ||
| "description": "Type of volume averaging for mask: 'mean', 'geomean' or 'max'", | ||
| "defaultValue": "geomean", | ||
| "options": [ | ||
| "mean", | ||
| "geomean", | ||
| "max" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "timepoints", | ||
| "type": "int", | ||
| "description": "Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation", | ||
| "defaultValue": 1000 | ||
| }, | ||
| { | ||
| "name": "f_hipass", | ||
| "type": "float", | ||
| "description": "Frequency (Hz) for high-pass filtering of cell timeseries", | ||
| "defaultValue": 0 | ||
| }, | ||
| { | ||
| "name": "f_volume", | ||
| "type": "float", | ||
| "description": "Imaging frequency in Hz", | ||
| "defaultValue": 2.0 | ||
| }, | ||
| { | ||
| "name": "n_cells_block", | ||
| "type": "int", | ||
| "description": "Number of cells in a block. Small number is fast but can lead to blocky output", | ||
| "defaultValue": 316 | ||
| }, | ||
| { | ||
| "name": "n_colors", | ||
| "type": "int", | ||
| "description": "Number of brain colors (2 in two-color volumes)", | ||
| "defaultValue": 1 | ||
| }, | ||
| { | ||
| "name": "res_x", | ||
| "type": "float", | ||
| "description": "X resolution in microns", | ||
| "defaultValue": 0.40625 | ||
| }, | ||
| { | ||
| "name": "res_y", | ||
| "type": "float", | ||
| "description": "Y resolution in microns", | ||
| "defaultValue": 0.40625 | ||
| }, | ||
| { | ||
| "name": "res_z", | ||
| "type": "float", | ||
| "description": "Z resolution in microns", | ||
| "defaultValue": 5.0 | ||
| }, | ||
| { | ||
| "name": "t_baseline", | ||
| "type": "int", | ||
| "description": "Interval for baseline calculation in seconds", | ||
| "defaultValue": 300 | ||
| }, | ||
| { | ||
| "name": "t_section", | ||
| "type": "float", | ||
| "description": "Exposure time in seconds for slice acquisition", | ||
| "defaultValue": 0.01 | ||
| }, | ||
| { | ||
| "name": "thr_mask", | ||
| "type": "float", | ||
| "description": "Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity)", | ||
| "defaultValue": 0.5 | ||
| }, | ||
| { | ||
| "name": "ext", | ||
| "type": "str", | ||
| "description": "File extension", | ||
| "defaultValue": ".nwb" | ||
| }, | ||
| { | ||
| "name": "dim_order", | ||
| "type": "str", | ||
| "description": "Dimensions order. Examples: 'zyx', 'xyz'", | ||
| "defaultValue": "xyz" | ||
| }, | ||
| { | ||
| "name": "remote", | ||
| "type": "bool", | ||
| "description": "Remote file", | ||
| "defaultValue": true | ||
| }, | ||
| { | ||
| "name": "output_to_nwb", | ||
| "type": "bool", | ||
| "description": "Save results to a new NWB file", | ||
| "defaultValue": true | ||
| } | ||
| ], | ||
| "attributes": [] | ||
| } | ||
| ] | ||
| } |