diff --git a/pom.xml b/pom.xml
index 5cafa5a2..70e3e6f7 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,7 +7,7 @@
ljp
functional-bioimage_core
- 1.4.7-SNAPSHOT
+ 1.5-SNAPSHOT
functional-bioimage-core
Bacteria Analyzer
diff --git a/src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java b/src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java
index 841ccc15..67eb6c05 100644
--- a/src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java
+++ b/src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java
@@ -60,7 +60,7 @@
import boa.plugins.plugins.processing_scheme.SegmentAndTrack;
import boa.plugins.plugins.processing_scheme.SegmentThenTrack;
import boa.plugins.plugins.segmenters.BacteriaIntensity;
-import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
+import boa.plugins.plugins.segmenters.MicrochannelFluo2D;
import boa.plugins.plugins.segmenters.MutationSegmenter;
import boa.plugins.plugins.trackers.MutationTracker;
import boa.plugins.plugins.trackers.MicrochannelTracker;
@@ -172,7 +172,7 @@ public static Experiment generateXPFluo(String name, String outputDir, boolean s
Structure mutation = new Structure("Mutation", 0, mutChan); // parent structure 1 segParentStructure 0
xp.getStructures().insert(mc, bacteria, mutation);
- mc.setProcessingScheme(new SegmentAndTrack(new MicrochannelTracker().setSegmenter(new MicroChannelFluo2D())));
+ mc.setProcessingScheme(new SegmentAndTrack(new MicrochannelTracker().setSegmenter(new MicrochannelFluo2D())));
//bacteria.setProcessingScheme(new SegmentAndTrack(new BacteriaClosedMicrochannelTrackerLocalCorrections(new BacteriaFluo()).setCostParameters(0.1, 0.5)));
bacteria.setProcessingScheme(new SegmentThenTrack(new BacteriaIntensity(), new BacteriaClosedMicrochannelTrackerLocalCorrections().setCostParameters(0.1, 0.5)));
mutation.setProcessingScheme(new SegmentAndTrack(
diff --git a/src/main/java/boa/core/generateXP/GenerateXP.java b/src/main/java/boa/core/generateXP/GenerateXP.java
index adab90f1..0fe955cd 100644
--- a/src/main/java/boa/core/generateXP/GenerateXP.java
+++ b/src/main/java/boa/core/generateXP/GenerateXP.java
@@ -66,7 +66,7 @@
import boa.plugins.plugins.processing_scheme.SegmentOnly;
import boa.plugins.plugins.processing_scheme.SegmentThenTrack;
import boa.plugins.plugins.segmenters.BacteriaIntensity;
-import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
+import boa.plugins.plugins.segmenters.MicrochannelFluo2D;
import boa.plugins.plugins.segmenters.MicrochannelPhase2D;
import boa.plugins.plugins.segmenters.MutationSegmenter;
import boa.plugins.plugins.thresholders.IJAutoThresholder;
@@ -479,8 +479,7 @@ public static void setParametersFluo(Experiment xp, boolean processing, boolean
mutation.setSegmentationParentStructure(1);
if (processing) {
mc.setProcessingScheme(new SegmentAndTrack(
- new MicrochannelTracker().setSegmenter(
- new MicroChannelFluo2D()
+ new MicrochannelTracker().setSegmenter(new MicrochannelFluo2D()
).setTrackingParameters(40, 0.5).setYShiftQuantile(0.05)
).addTrackPostFilters(new RemoveMicrochannelsTouchingBackgroundOnSides(2),
new RemoveMicrochannelsWithOverexpression(99, 5).setTrim(true),
diff --git a/src/main/java/boa/plugins/PluginFactory.java b/src/main/java/boa/plugins/PluginFactory.java
index 37a80e32..39ca9328 100644
--- a/src/main/java/boa/plugins/PluginFactory.java
+++ b/src/main/java/boa/plugins/PluginFactory.java
@@ -46,7 +46,7 @@ public class PluginFactory {
private final static TreeMap plugins = new TreeMap<>();
private final static Logger logger = LoggerFactory.getLogger(PluginFactory.class);
- private final static Map refactoredNamesOldMapNew = new HashMap(){{put("BacteriaFluo", "BacteriaIntensity");}};
+ private final static Map refactoredNamesOldMapNew = new HashMap(){{put("BacteriaFluo", "BacteriaIntensity");put("MicroChannelFluo2D", "MicrochannelFluo2D");put("LAPTracker", "MutationTracker");put("MutationSegmenter", "MutationSegmenter");}};
public static void findPlugins(String packageName) {
logger.info("looking for plugin in package: {}", packageName);
diff --git a/src/main/java/boa/plugins/plugins/segmenters/MicroChannelFluo2D.java b/src/main/java/boa/plugins/plugins/segmenters/MicrochannelFluo2D.java
similarity index 97%
rename from src/main/java/boa/plugins/plugins/segmenters/MicroChannelFluo2D.java
rename to src/main/java/boa/plugins/plugins/segmenters/MicrochannelFluo2D.java
index 8bcadf5f..3e939848 100644
--- a/src/main/java/boa/plugins/plugins/segmenters/MicroChannelFluo2D.java
+++ b/src/main/java/boa/plugins/plugins/segmenters/MicrochannelFluo2D.java
@@ -55,7 +55,7 @@
*
* @author jollion
*/
-public class MicroChannelFluo2D implements MicrochannelSegmenter, TrackParametrizable, ToolTip {
+public class MicrochannelFluo2D implements MicrochannelSegmenter, TrackParametrizable, ToolTip {
NumberParameter channelHeight = new BoundedNumberParameter("Microchannel Height", 0, 430, 5, null).setToolTipText("Height of microchannel in pixels");
NumberParameter channelWidth = new BoundedNumberParameter("Microchannel Width", 0, 40, 5, null);
@@ -69,9 +69,9 @@ public class MicroChannelFluo2D implements MicrochannelSegmenter, TrackParametri
+ "- Rough segmentation of cells using \"Threshold\" computed the whole track prior to segmentation step
"
+ "- Selection of filled channels: lengh in X direction should be over \"Microchannel Height\" x \"Microchannel filling proportion\"
"
+ "- Computation of Y start: min value of the min y coordinate of the selected objects at step 2