exposed intensity method parameter for RS-FISH

Author: krokicki

containers/rs_fish/Dockerfile

@@ -2,7 +2,7 @@
 # Dockerfile generated by Maru 0.1.1
 
 # Staged build using builder container
-FROM janeliascicomp/builder:1.2.1 as builder
+FROM janeliascicomp/builder:1.3.1 as builder
 ARG GIT_TAG=main
 
 # Checkout and build the code

containers/rs_fish/maru.yaml

@@ -1,12 +1,12 @@
 maru_version: 0.1.1
 name: rs_fish
-version: 1.0.1
+version: 1.0.2
 remotes:
 - multifish
 - registry.int.janelia.org/multifish
 - public.ecr.aws/janeliascicomp/multifish
 build_args:
-  GIT_TAG: main
+  GIT_TAG: 0.0.2
 template_args:
   flavor: java_maven
   build:

docs/Parameters.md

@@ -152,6 +152,7 @@ Options for the RS-FISH spot extraction algorithm
 |`rsfish_sigma`|Sigma value for Difference-of-Gaussian (DoG) calculation. Default 1.5||`number`
 |`rsfish_threshold`|Threshold value for Difference-of-Gaussian (DoG) calculation. Default: 0.007||`number`
 |`rsfish_background`|Background subtraction method, 0 == None, 1 == Mean, 2==Median, 3==RANSAC on Mean, 4==RANSAC on Median. Default: 0 (None)||`integer`
+|`rsfish_intensity`|Intensity calculation method, 0 == Linear Interpolation, 1 == Gaussian fit (on inlier pixels), 2 == Integrate spot intensities (on candidate pixels). Default: 0 (Linear Interpolation)||`integer`
 |`rsfish_params`|Any other parameters to pass to the RS-FISH algorithm.|Complete parameter documentation for RS-FISH is [available here](https://github.com/PreibischLab/RS-FISH-Spark/blob/main/src/main/java/net/preibisch/rsfish/spark/SparkRSFISH.java).|`string`
 |`rsfish_workers`|Number of Spark workers to use for RS-FISH spot detection. Default: 4||`integer`
 |`rsfish_worker_cores`|Number of cores allocated to each RS-FISH Spark worker. Default: 4||`integer`
@@ -161,7 +162,7 @@ Options for the RS-FISH spot extraction algorithm
 
 ### Per channel RS-FISH Parameters
 
-The following parameters can be set per channel: `rsfish_min`, `rsfish_max`, `rsfish_anisotropy`, `rsfish_sigma`, `rsfish_threshold`, `rsfish_background`. For that simply prefix the corresponding parameter with `--per_channel.` and set the values using a comma delimited list. The values will be associated with the corresponding channel based on their position, i.e. first value will be associated with the first channel, second with the second channel, etc. If a value is missing or empty the parameter value for the channel will be set to the default from the parameter with the same name (presented above).
+The following parameters can be set per channel: `rsfish_min`, `rsfish_max`, `rsfish_anisotropy`, `rsfish_sigma`, `rsfish_threshold`, `rsfish_background`, `rsfish_intensity`. Simply prefix the corresponding parameter with `per_channel.` and set the values using a comma delimited list. The values will be associated with the corresponding channel based on their position, i.e. first value will be associated with the first channel, second with the second channel, etc. If a value is missing or empty the parameter value for the channel will be set to the default from the parameter with the same name (presented above).
 
 For example if the command like is:
 `--channels c0,c1,c2,c3 --sigma 1.7 --per_channel.sigma "1.2,,1.4`

nextflow_schema.json

@@ -543,6 +543,11 @@
                     "description": "Background subtraction method, 0 == None, 1 == Mean, 2==Median, 3==RANSAC on Mean, 4==RANSAC on Median. Default: 0 (None)",
                     "fa_icon": "fas fa-level-down-alt"
                 },
+                "rsfish_intensity": {
+                    "type": "integer",
+                    "description": "Intensity calculation method, 0 == Linear Interpolation, 1 == Gaussian fit (on inlier pixels), 2 == Integrate spot intensities (on candidate pixels). Default: 0 (Linear Interpolation)",
+                    "fa_icon": "fas fa-level-down-alt"
+                },
                 "per_channel.rsfish_min": {
                   "type": "string",
                   "description": "Comma delimited per channel values for rsfish_min",
@@ -573,6 +578,11 @@
                   "description": "Comma delimited per channel values for rsfish_background",
                   "fa_icon": "fas fa-terminal"
                 },
+                "per_channel.rsfish_intensity": {
+                  "type": "string",
+                  "description": "Comma delimited per channel values for rsfish_intensity",
+                  "fa_icon": "fas fa-terminal"
+                },
                 "rsfish_params": {
                     "type": "string",
                     "description": "Any other parameters to pass to the RS-FISH algorithm.",

param_utils.nf

@@ -73,7 +73,7 @@ def default_mf_params() {
         use_rsfish: false,
         rsfish_container_repo: multifish_container_repo,
         rsfish_container_name: 'rs_fish',
-        rsfish_container_version: '1.0.1',
+        rsfish_container_version: '1.0.2',
         rs_fish_app: '/app/app.jar',
         rsfish_workers: 6,
         rsfish_worker_cores: 8,
@@ -86,6 +86,7 @@ def default_mf_params() {
         rsfish_sigma: 1.5,
         rsfish_threshold: 0.007,
         rsfish_background: 0,
+        rsfish_intensity: 0,
         rsfish_params: '',
         // RS-Fish parameters adjustable per channel
         per_channel: [
@@ -95,6 +96,7 @@ def default_mf_params() {
             rsfish_sigma: '',
             rsfish_threshold: '',
             rsfish_background: '',
+            rsfish_intensity: '',
         ],
 
         // segmentation params

workflows/rs_fish.nf

@@ -81,6 +81,7 @@ workflow rsfish {
         def sigma = all_per_channels_params.rsfish_sigma[channel]
         def threshold = all_per_channels_params.rsfish_threshold[channel]
         def background = all_per_channels_params.rsfish_background[channel]
+        def intensity = all_per_channels_params.rsfish_intensity[channel]
         def rsfish_cmd_args = [
             "--image=${input_dir} --dataset=${subpath} " +
             "--minIntensity=${minIntensity} " +
@@ -89,6 +90,7 @@ workflow rsfish {
             "--sigma=${sigma} " +
             "--threshold=${threshold} " +
             "--background=${background} " +
+            "--intensityMethod=${intensity} " +
             "--output=${output_voxel_file} ${params.rsfish_params}",
             cluster_work_dir,
             "rsFISH_${acq_name}_${channel}.log",
@@ -156,6 +158,7 @@ def get_all_per_channel_params(Map ps) {
         rsfish_sigma: get_param_values_per_channel(ps, 'rsfish_sigma'),
         rsfish_threshold: get_param_values_per_channel(ps, 'rsfish_threshold'),
         rsfish_background: get_param_values_per_channel(ps, 'rsfish_background'),
+        rsfish_intensity: get_param_values_per_channel(ps, 'rsfish_intensity'),
     ]
 }