From 865440260f45b9fb99fd1c9f375d1fdbbdb75dff Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 19 Nov 2024 17:52:57 +0000 Subject: [PATCH] update spec.json --- voluseg/main.py | 0 voluseg/spec.json | 211 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 211 insertions(+) mode change 100644 => 100755 voluseg/main.py create mode 100644 voluseg/spec.json diff --git a/voluseg/main.py b/voluseg/main.py old mode 100644 new mode 100755 diff --git a/voluseg/spec.json b/voluseg/spec.json new file mode 100644 index 0000000..af6ba74 --- /dev/null +++ b/voluseg/spec.json @@ -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": [] + } + ] +} \ No newline at end of file