";
+ else
+ htmlText = strjoin(htmlLines, newline);
+ end
+
+ function flushParagraph()
+ if isempty(paragraphLines)
+ return
+ end
+ paragraphText = strjoin(paragraphLines, " ");
+ htmlLines(end+1, 1) = "
" + formatInlineGuideText(paragraphText) + "
";
+ paragraphLines = strings(0, 1);
+ end
+
+ function flushListItem()
+ if isempty(listItemLines)
+ return
+ end
+ itemText = strjoin(listItemLines, " ");
+ htmlLines(end+1, 1) = "
" + formatInlineGuideText(itemText) + "
"; %#ok
+ listItemLines = strings(0, 1);
+ end
+
+ function closeList()
+ if isInList
+ htmlLines(end+1, 1) = "
";
+ isInList = false;
+ end
+ end
+end
+
+function tf = isGuideHeading(line)
+ tf = endsWith(line, ":") && strlength(line) <= 80 && ~contains(line, "://");
+end
+
+function tf = isRawHtmlLine(line)
+ htmlPrefixes = ["$1');
+end
+
+function htmlText = escapeHtml(text)
+ htmlText = replace(text, "&", "&");
+ htmlText = replace(htmlText, "<", "<");
+ htmlText = replace(htmlText, ">", ">");
+end
+
+function flatStruct = flattenNestedStruct(nestedStruct, parentName)
+ % Recursively flattens a nested struct into a struct with 'name' and 'default_value'
+ % where nested fields are joined with "."
+ %
+ % Inputs:
+ % nestedStruct - The nested struct to flatten
+ % parentName - (Optional) The parent field name for recursion
+ %
+ % Outputs:
+ % flatStruct - The resulting flat struct with fields 'name' and 'default_value'
+
+ if nargin < 2
+ parentName = '';
+ end
+
+ flatStruct = struct('name', {}, 'default_value', {}, 'description', {});
+ fieldNames = fieldnames(nestedStruct);
+
+ for i = 1:numel(fieldNames)
+ if endsWith(fieldNames{i}, '_')
+ continue
+ end
+
+ fieldName = fieldNames{i};
+ fullName = fieldName;
+ if ~isempty(parentName)
+ fullName = sprintf('%s.%s', parentName, fieldName);
+ end
+
+ value = nestedStruct.(fieldName);
+ if isstruct(value)
+ % Recurse into nested structs
+ nestedFlatStruct = flattenNestedStruct(value, fullName);
+ flatStruct = [flatStruct, nestedFlatStruct];
+ else
+ if ischar(value)
+ % pass
+ elseif isempty(value)
+ value = '';
+ elseif isscalar(value)
+ value = formatValueAsString(value);
+ else
+ if iscell(value)
+ value = cellfun(@(c) formatValueAsString(c), value, 'uni', false);
+ value = sprintf('{%s}', strjoin(value, ', '));
+ else
+ value = arrayfun(@(c) formatValueAsString(c), value, 'uni', false);
+ value = sprintf('[%s]', strjoin(value, ', '));
+ end
+ end
+
+ % Add field to flatStruct
+ flatStruct(end + 1).name = fullName;
+ flatStruct(end).default_value = value;
+ flatStruct(end).description = 'No description available.';
+ end
+ end
+end
+
+
+function value = formatValueAsString(value)
+ if isinteger(value)
+ value = sprintf('%d', value);
+ elseif isnumeric(value)
+ value = sprintf('%.2f', value);
+ elseif islogical(value)
+ if value
+ value = 'true';
+ else
+ value = 'false';
+ end
+ end
+end
diff --git a/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/+organize/changeDataLocationRoot.m b/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/+organize/changeDataLocationRoot.m
index 3aeb23c73..4cb681e30 100644
--- a/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/+organize/changeDataLocationRoot.m
+++ b/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/+organize/changeDataLocationRoot.m
@@ -1,6 +1,10 @@
function varargout = changeDataLocationRoot(sessionObject, varargin)
-%CHANGERAWDATAROOT Summary of this function goes here
-% Detailed explanation goes here
+%CHANGEDATALOCATIONROOT Change the root directory for the specified data location of a session.
+%
+% CHANGEDATALOCATIONROOT opens an interactive dialog for changing the root
+% folder of the selected data location for a session. The dialog is a
+% dropdown selector where you can select the root folder from all
+% configured root folders of the data location.
% % % % % % % % % % % % % % % INSTRUCTIONS % % % % % % % % % % % % % % %
% - - - - - - - - - - You can remove this part - - - - - - - - - - -
diff --git a/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/backup.m b/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/backup.m
index 98348a124..390f03d72 100644
--- a/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/backup.m
+++ b/code/modules/+nansen/+module/+general/+core/+sessionmethod/+data/backup.m
@@ -1,7 +1,7 @@
function varargout = backup(sessionObject, varargin)
-%backup Backup a session folder for a specific data location
+%BACKUP Backup a session folder for the specified data location
%
-% backup(sessionObject) backs up data for the selected data location.
+% BACKUP backs up data for the selected data location of a session.
% Todo:
% [ ] Add mirror mode. (I.e delete files in target that are missing )
@@ -119,10 +119,10 @@
%getDefaultParameters Define the default parameters for this function
params = struct();
- params.BackupMode = 'merge (no replace)';
+ params.BackupMode = 'merge (no replace)'; % Mode for backup. Options: "merge (no replace)", "only replace files if newer", "replace all files"
params.BackupMode_ = {'merge (no replace)', 'only replace files if newer', 'replace all files'};
- params.BackupLocation = '';
+ params.BackupLocation = ''; % Absolute path to folder where data should be backed up
params.BackupLocation_ = 'uigetdir';
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/deltaFOverF.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/deltaFOverF.m
index 089b208e9..3001218f0 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/deltaFOverF.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/deltaFOverF.m
@@ -1,6 +1,16 @@
function varargout = deltaFOverF(sessionObject, varargin)
-%deltaFOverF Summary of this function goes here
-% Detailed explanation goes here
+%View delta-F-over-F ROI signals for this session.
+%
+%Use this when:
+%- You have already run signal extraction and delta-F-over-F computation.
+%- You want to inspect normalized ROI activity traces in SignalViewer.
+%
+%What happens:
+%- NANSEN checks that `RoiSignals_Dff` exists for the selected session.
+%- The `RoiSignals_Dff` column is opened in the interactive SignalViewer app.
+%
+%Outputs:
+%- No data are written; this method only opens an interactive viewer.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -28,7 +38,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
sessionObject.validateVariable('RoiSignals_Dff')
roiSignalArray = sessionObject.loadData('RoiSignals_Dff');
@@ -41,6 +51,5 @@
function S = getDefaultParameters()
S = struct();
- % Add more fields:
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/imageStack.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/imageStack.m
index 874c2b374..28a3d4cde 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/imageStack.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/imageStack.m
@@ -1,21 +1,19 @@
function varargout = imageStack(sessionObj, varargin)
-%imageStack Open image stack data variable in imviewer
+%Open any image-stack data variable from this session in imviewer.
%
-% imageStack(sessionObj) opens the first imagestack variable for
-% the given session using default options.
+%Use this when:
+%- You want to inspect an ImageStack variable without running processing.
+%- You need to choose between raw, motion-corrected, denoised, downsampled,
+% or other ImageStack variables registered in the active variable model.
%
-% imageStack(sessionObj, Name, Value) opens an imagestack using
-% the options given as name, value pairs.
+%What happens:
+%- NANSEN builds one menu alternative for each ImageStack variable.
+%- With `UseVirtualStack` enabled, imviewer reads frames lazily from disk.
+%- With `UseVirtualStack` disabled, only `FirstImage` through `LastImage`
+% are loaded into memory before opening imviewer.
%
-% fcnAttributes = imageStack() returns a struct of attributes for
-% the function.
-%
-% List of options (name, value pairs):
-%
-% VariableName : Name of data variable to open in imviewer
-% UseVirtualStack : Boolean flag, open using virtual stack or not
-% FirstImage : First image to load (if UseVirtualStack is false)
-% LastImage : Last image to load (if UseVirtualStack is false)
+%Outputs:
+%- No data are written; this method only opens an interactive viewer.
import nansen.session.SessionMethod
@@ -73,9 +71,9 @@
%getDefaultParameters Define the default parameters for this function
S = struct();
- S.UseVirtualStack = true;
- S.FirstImage = 1;
- S.LastImage = inf;
+ S.UseVirtualStack = true; % Open the stack lazily from disk when possible.
+ S.FirstImage = 1; % First frame to load when UseVirtualStack is false.
+ S.LastImage = inf; % Last frame to load when UseVirtualStack is false.
end
function alternatives = getVariableNameAlternatives()
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/meanFluorescence.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/meanFluorescence.m
index 6df7f7c0c..24865a042 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/meanFluorescence.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/meanFluorescence.m
@@ -1,6 +1,17 @@
function varargout = meanFluorescence(sessionObject, varargin)
-%meanFluorescence Summary of this function goes here
-% Detailed explanation goes here
+%View extracted mean-fluorescence ROI signals for this session.
+%
+%Use this when:
+%- You have already extracted ROI signals from the motion-corrected stack.
+%- You want to inspect raw fluorescence traces before neuropil correction,
+% delta-F-over-F computation, or deconvolution.
+%
+%What happens:
+%- NANSEN loads `RoiSignals_MeanF`.
+%- The signals are opened in the interactive SignalViewer app.
+%
+%Outputs:
+%- No data are written; this method only opens an interactive viewer.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -11,7 +22,7 @@
params = getDefaultParameters();
% Create a cell array with attribute keywords
- ATTRIBUTES = {'batch', 'unqueueable'};
+ ATTRIBUTES = {'serial', 'unqueueable', 'MethodName', 'View Mean Fluorescence'};
% % % % % % % % % % % % % DEFAULT CODE BLOCK % % % % % % % % % % % % % %
% - - - - - - - - - - Please do not edit this part - - - - - - - - - - -
@@ -28,7 +39,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
sessionObject.validateVariable('RoiSignals_MeanF')
roiSignalArray = sessionObject.loadData('RoiSignals_MeanF');
@@ -39,6 +50,5 @@
function S = getDefaultParameters()
S = struct();
- % Add more fields:
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonMotionCorrected.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonMotionCorrected.m
index 768d3cc21..39df1ef15 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonMotionCorrected.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonMotionCorrected.m
@@ -1,14 +1,19 @@
function varargout = twoPhotonMotionCorrected(sessionObj, varargin)
-%twoPhotonMotionCorrected Open 2-photon corrected recording in imviewer
+%View the motion-corrected two-photon recording in imviewer.
%
-% twoPhotonMotionCorrected(sessionObj) opens the motion-corrected
-% two-photon recording for the given session using default options.
+%Use this when:
+%- You want to inspect the registered recording after motion correction.
+%- You need a quick quality-control pass before ROI detection or signal
+% extraction.
%
-% twoPhotonMotionCorrected(sessionObj, Name, Value) opens the recording
-% using the options given as name, value pairs.
+%What happens:
+%- NANSEN opens `TwoPhotonSeries_Corrected` for the selected session.
+%- With `UseVirtualStack` enabled, imviewer reads frames lazily from disk.
+%- With `UseVirtualStack` disabled, only `FirstImage` through `LastImage`
+% are loaded into memory before opening imviewer.
%
-% fcnAttributes = twoPhotonMotionCorrected() returns a struct of
-% attributes for the function.
+%Outputs:
+%- No data are written; this method only opens an interactive viewer.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Please create a struct of default parameters (if applicable) and specify
@@ -17,7 +22,7 @@
% % % Get struct of default parameters for function.
params = getDefaultParameters();
- ATTRIBUTES = {'serial', 'unqueueable'};
+ ATTRIBUTES = {'serial', 'unqueueable', 'MethodName', 'View Motion-Corrected 2-Photon'};
% % % % % % % % % % % % % DEFAULT CODE BLOCK % % % % % % % % % % % % % %
% - - - - - - - - - - Please do not edit this part - - - - - - - - - - -
@@ -51,10 +56,9 @@
end
end
-function S = getDefaultParameters()
- S = struct();
- S.UseVirtualStack = true;
- S.FirstImage = 1;
- S.LastImage = inf;
-
+function params = getDefaultParameters()
+ params = struct();
+ params.UseVirtualStack = true; % Whether to open the stack without loading data into memory (virtual stack).
+ params.FirstImage = uint64(1); % Index of first frame to load if UseVirtualStack is false
+ params.LastImage = inf; % Index of last frame to load if UseVirtualStack is false
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonRawImages.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonRawImages.m
index aec1f51f0..4e2072847 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonRawImages.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+data/+openInViewer/twoPhotonRawImages.m
@@ -1,14 +1,21 @@
function varargout = twoPhotonRawImages(sessionObj, varargin)
-%twoPhotonRawImages Open 2-photon raw recording in imviewer
+%View the original two-photon recording in imviewer.
%
-% twoPhotonRawImages(sessionObj) opens the raw two-photon recording for
-% the given session using default options.
+%Use this when:
+%- You want to inspect the raw recording before motion correction.
+%- You need to check imaging quality, drift, motion, flyback lines, or
+% acquisition artifacts in the source data.
%
-% twoPhotonRawImages(sessionObj, Name, Value) opens the recording using
-% the options given as name, value pairs.
+%What happens:
+%- NANSEN opens `TwoPhotonSeries_Original` for the selected session.
+%- With `UseVirtualStack` enabled, imviewer reads frames lazily from disk.
+%- With `UseVirtualStack` disabled, only `FirstImage` through `LastImage`
+% are loaded into memory before opening imviewer.
+%- If a recording contains multiple FOV stacks, you are prompted to choose
+% which FOVs to open.
%
-% fcnAttributes = twoPhotonRawImages() returns a struct of attributes for
-% the function.
+%Outputs:
+%- No data are written; this method only opens an interactive viewer.
% Todo: Implement dynamic retrieval of parameters based on file adapter
% for opening files.
@@ -20,7 +27,7 @@
% % % Get struct of default parameters for function.
params = getDefaultParameters();
- ATTRIBUTES = {'serial', 'unqueueable'};
+ ATTRIBUTES = {'serial', 'unqueueable', 'MethodName', 'View Original (Raw) 2-Photon'};
% % % % % % % % % % % % % DEFAULT CODE BLOCK % % % % % % % % % % % % % %
% - - - - - - - - - - Please do not edit this part - - - - - - - - - - -
@@ -70,9 +77,9 @@
end
end
-function S = getDefaultParameters()
- S = struct();
- S.UseVirtualStack = true;
- S.FirstImage = 1;
- S.LastImage = inf;
+function params = getDefaultParameters()
+ params = struct();
+ params.UseVirtualStack = true; % Open the stack lazily from disk when possible.
+ params.FirstImage = uint64(1); % First frame to load when UseVirtualStack is false.
+ params.LastImage = inf; % Last frame to load when UseVirtualStack is false.
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+plot/plotImageStats.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+plot/plotImageStats.m
index ed684ccd4..5ce2c3011 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+plot/plotImageStats.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+plot/plotImageStats.m
@@ -1,8 +1,19 @@
function varargout = plotImageStats(sessionObj, varargin)
-%plotImageStats Plot stats from raw two photon recording
+%Plot frame-wise image statistics for a two-photon recording.
%
-% Plot mean pixel value for each frame with a shaded error bar
-% corresponding to a lower and an upper percentile of the pixel values.
+%Use this when:
+%- You want a fast quality-control view of brightness, saturation, or
+% acquisition instability across time.
+%- You have an `ImageStats` data variable for the selected session.
+%
+%What happens:
+%- NANSEN loads `ImageStats` and plots the mean pixel value per frame in
+% SignalViewer.
+%- Optional shaded envelopes show the minimum/maximum range and configured
+% percentile ranges.
+%
+%Outputs:
+%- No data are written; this method only opens an interactive plot.
% % % Get struct of default parameters for function.
params = getDefaultParameters();
@@ -40,6 +51,7 @@
axes(hViewer.Axes)
if params.ShowExtremes
+ assertHasShadedErrorBar()
lowerBound = (S.meanValue - S.minimumValue)';
upperBound = (S.maximumValue - S.meanValue)';
h = shadedErrorBar([], S.meanValue, [upperBound; lowerBound], 'lineprops',{'color', cmap(:,1)});
@@ -52,6 +64,7 @@
uistack(hLine, 'top')
if params.ShowPrctile1
+ assertHasShadedErrorBar()
lowerBound = (S.meanValue - S.prctileL1)';
upperBound = (S.prctileU1 - S.meanValue)';
h = shadedErrorBar([], S.meanValue, [upperBound; lowerBound], 'lineprops',{'color', cmap(:,2)});
@@ -61,6 +74,7 @@
uistack(hLine, 'top')
if params.ShowPrctile2
+ assertHasShadedErrorBar()
lowerBound = (S.meanValue - S.prctileL2)';
upperBound = (S.prctileU2 - S.meanValue)';
h = shadedErrorBar([], S.meanValue, [upperBound; lowerBound], 'lineprops',{'color', cmap(:,3)});
@@ -73,7 +87,12 @@
function params = getDefaultParameters()
params = struct();
- params.ShowExtremes = true;
- params.ShowPrctile1 = true;
- params.ShowPrctile2 = true;
+ params.ShowExtremes = true; % Show the minimum-to-maximum pixel range.
+ params.ShowPrctile1 = true; % Show the first configured percentile envelope.
+ params.ShowPrctile2 = true; % Show the second configured percentile envelope.
end
+
+function assertHasShadedErrorBar()
+ assert( exist('shadedErrorBar', 'file') == 2, ...
+ 'This method requires shadedErrorBar from MATLAB FileExchange')
+end
\ No newline at end of file
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/EXTRACT.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/EXTRACT.m
index b23159686..f2058b73a 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/EXTRACT.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/EXTRACT.m
@@ -1,6 +1,25 @@
classdef EXTRACT < nansen.session.SessionMethod & nansen.wrapper.extract.Processor
-%EXTRACT Summary of this function goes here
-% Detailed explanation goes here
+%Detect ROIs automatically with EXTRACT.
+%
+%Use this when:
+%- You want automated ROI detection on `TwoPhotonSeries_Corrected`.
+%- You expect EXTRACT's calcium-imaging model to be a better fit than
+% Quicky or suite2p for the current recording.
+%
+%What happens:
+%- NANSEN loads the motion-corrected stack and opens it as the source stack
+% for the EXTRACT wrapper.
+%- EXTRACT is run through the NANSEN ROI segmentation pipeline, including
+% chunking, result merging, ROI-image computation, and ROI-statistics
+% computation.
+%
+%Outputs:
+%- `roiArrayExtractAuto`: automatically detected ROIs.
+%- `ExtractOptions`, `ExtractResultsTemp`, and `ExtractResultsFinal` are
+% saved as method outputs for provenance and restart support.
+%
+%Reference:
+%- https://github.com/schnitzer-lab/EXTRACT-public
properties (Constant) % SessionMethod attributes
BatchMode = 'serial' % Move to data method?
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/Quicky.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/Quicky.m
index 545b01617..0129f5ed0 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/Quicky.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/Quicky.m
@@ -1,6 +1,26 @@
classdef Quicky < nansen.session.SessionMethod & nansen.wrapper.quicky.Processor
-%QUICKY Summary of this function goes here
-% Detailed explanation goes here
+%Detect ROIs automatically with Quicky.
+%
+%Use this when:
+%- You want a fast automated segmentation pass on `TwoPhotonSeries_Corrected`.
+%- Your data are similar to the Thy1-GCaMP6s recordings this method was
+% developed around in the Vervaeke Lab.
+%
+%What happens:
+%- NANSEN loads the motion-corrected stack and opens it as the source stack
+% for the Quicky wrapper.
+%- Quicky is run through the NANSEN ROI segmentation pipeline, including
+% chunking, result merging, ROI-image computation, and ROI-statistics
+% computation.
+%
+%Outputs:
+%- `roiArrayQuickyAuto`: automatically detected ROIs.
+%- `QuickyOptions` and intermediate Quicky result files are saved for
+% provenance and restart support.
+%
+%Limitations:
+%- Quicky is tuned for a specific data style and may not generalize as well
+% to other preparations, indicators, or imaging systems.
properties (Constant) % SessionMethod attributes
BatchMode = 'serial' % Move to data method?
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/suite2p.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/suite2p.m
index e325070a9..60824f0d5 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/suite2p.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+autoSegmentation/suite2p.m
@@ -1,6 +1,23 @@
classdef suite2p < nansen.session.SessionMethod & nansen.wrapper.suite2p.Processor
-%EXTRACT Summary of this function goes here
-% Detailed explanation goes here
+%Detect ROIs automatically with suite2p.
+%
+%Use this when:
+%- You want to run suite2p ROI detection on `TwoPhotonSeries_Corrected`
+% from inside the NANSEN session workflow.
+%- You want suite2p results saved back into the session data model rather
+% than managed only in an external suite2p output folder.
+%
+%What happens:
+%- NANSEN loads the motion-corrected stack and opens it as the source stack
+% for the suite2p wrapper.
+%- suite2p is run through the NANSEN ROI segmentation pipeline, including
+% chunking, component merging, ROI-image computation, and ROI-statistics
+% computation.
+%
+%Outputs:
+%- `roiArraySuite2pAuto`: automatically detected ROIs.
+%- `Suite2pOptions`, `Suite2pResultsTemp`, and `Suite2pResultsFinal` are
+% saved as method outputs for provenance and restart support.
properties (Constant) % SessionMethod attributes
BatchMode = 'serial' % Move to data method?
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+deconvolution/Caiman.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+deconvolution/Caiman.m
index 078f1e677..f5d7c7795 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+deconvolution/Caiman.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+deconvolution/Caiman.m
@@ -1,6 +1,22 @@
classdef Caiman < nansen.session.SessionMethod
-%DeconvolutionCaImAn Summary of this function goes here
-% Detailed explanation goes here
+%Deconvolve delta-F-over-F traces with the CaImAn signal model.
+%
+%Use this when:
+%- You have already computed `RoiSignals_Dff`.
+%- You want denoised and event-like deconvolved traces for downstream
+% analysis or inspection.
+%
+%What happens:
+%- NANSEN loads `RoiSignals_Dff`.
+%- The selected CaImAn deconvolution parameters are applied to each ROI
+% trace.
+%- Preview mode opens the deconvolution explorer so parameters can be tuned
+% before committing the run.
+%
+%Outputs:
+%- `RoiSignals_Deconvolved`: deconvolved ROI activity estimates.
+%- `RoiSignals_Denoised`: denoised delta-F-over-F traces.
+%- `OptionsDeconvolution`: the options used for this run.
properties (Constant) % SessionMethod attributes
MethodName = 'Deconvolution CaImAn'
@@ -17,7 +33,7 @@
methods (Static)
function options = getDefaultOptions()
- %GETDEFAULTOPTIONS Summary of this function goes here
+ %GETDEFAULTOPTIONS Return default CaImAn deconvolution options.
options = nansen.twophoton.roisignals.getDeconvolutionParameters();
end
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DenoiseStack.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DenoiseStack.m
index 542d9ab2a..7cc37ab31 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DenoiseStack.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DenoiseStack.m
@@ -1,31 +1,26 @@
function varargout = DenoiseStack(sessionObject, varargin)
-%DenoiseStack Denoise an ImageStack using the DeepInterpolation method
+%Denoise an image stack with DeepInterpolation.
%
-% This method is based on the DeepInterpolation method from the Allen
-% Institute. It requires MATLAB 2023a or later and the external toolbox
-% "Deep Learning Toolbox Converter for TensorFlow Models".
+%Use this when:
+%- You want to suppress frame-wise noise in an ImageStack before visual
+% inspection or downstream processing.
+%- You have MATLAB R2023a or newer and the Deep Learning Toolbox Converter
+% for TensorFlow Models available.
%
-% Note: Currently it uses the tretrained model they provided for two-photon
-% data. It is possible to train models (See the DeepInterpolation_Matlab)
-% on GitHub for details. Create an issue on VervaekeLab/Nansen if you
-% need help adapting the code to run with another model.
+%What happens:
+%- You choose which ImageStack variable to denoise.
+%- NANSEN runs the stack denoiser with the configured DeepInterpolation
+% window and stack-processing options.
+%- The current implementation uses the pretrained two-photon model from the
+% DeepInterpolation MATLAB workflow.
%
-% Input:
-% Input must be an ImageStack
+%Outputs:
+%- A denoised stack is produced by the stack processor according to the
+% selected export options.
%
-% Options:
-% PrePostOmission : How many frames around the target frame to omit
-% for the interpolation. Default = 0.
-%
-% PreFrame : How many frames before the target frame to use for
-% interpolation. Default = 30.
-%
-% PostFrame : How many frames after the target frame to use for
-% interpolation. Default = 30.
-%
-% References:
-% (1) https://github.com/AllenInstitute/deepinterpolation
-% (2) https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB
+%References:
+%- https://github.com/AllenInstitute/deepinterpolation
+%- https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -53,7 +48,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
imageStack = sessionObject.loadData(params.Input.VariableName);
params = utility.struct.renamefield(params, 'StackOptions', 'Run');
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DownsampleStack.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DownsampleStack.m
index 65ee8a949..f8a9c8aa0 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DownsampleStack.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+imageProcessing/DownsampleStack.m
@@ -1,6 +1,20 @@
function varargout = DownsampleStack(sessionObject, varargin)
-%DOWNSAMPLESTACK Summary of this function goes here
-% Detailed explanation goes here
+%Create a temporally downsampled copy of an image stack.
+%
+%Use this when:
+%- You need a smaller stack for quick inspection, algorithm testing, or
+% lightweight downstream processing.
+%- You want to bin frames over time while preserving the original image
+% height, width, channel count, and data type.
+%
+%What happens:
+%- NANSEN loads the selected stack variable.
+%- Consecutive groups of frames are binned with the selected method.
+%- The downsampled stack is saved to file by the stack processor.
+%
+%Outputs:
+%- A temporally downsampled ImageStack file is created according to the
+% selected downsampling factor and binning method.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -28,7 +42,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
imageStack = sessionObject.loadData(params.StackName);
@@ -46,10 +60,10 @@
function S = getDefaultParameters()
S = struct();
- S.StackName = 'TwoPhotonSeries_Corrected';
+ S.StackName = 'TwoPhotonSeries_Corrected'; % ImageStack variable to downsample.
S.StackName_ = {'TwoPhotonSeries_Corrected'};
- S.DownsamplingFactor = 10;
- S.BinningMethod = 'mean';
+ S.DownsamplingFactor = 10; % Number of consecutive frames per output frame.
+ S.BinningMethod = 'mean'; % Method used to combine frames within each bin.
S.BinningMethod_ = {'mean', 'max'};
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/flowreg.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/flowreg.m
index 44a884369..9e9f78be8 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/flowreg.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/flowreg.m
@@ -1,6 +1,26 @@
classdef flowreg < nansen.session.SessionMethod & nansen.wrapper.flowreg.Processor
-%normcorre Summary of this function goes here
-% Detailed explanation goes here
+%Motion-correct the raw two-photon recording with FlowRegistration.
+%
+%Use this when:
+%- You want non-rigid motion correction using the FlowRegistration toolbox.
+%- You need motion-corrected data plus diagnostic projections and movement
+% statistics saved back into the session.
+%
+%What happens:
+%- NANSEN loads `TwoPhotonSeries_Original` and enables stack preprocessing.
+%- FlowRegistration estimates frame shifts and writes the corrected stack.
+%- Reference images, projections, and correction statistics are generated
+% by the shared motion-correction pipeline.
+%
+%Outputs:
+%- `TwoPhotonSeries_Corrected`: motion-corrected image stack.
+%- `FlowregOptions` and `FlowregShifts`: method-specific settings and
+% frame shifts.
+%- Motion-correction QC outputs such as `FovAverageProjection`,
+% `FovMaximumProjection`, and `MotionCorrectionStats`.
+%
+%Reference:
+%- https://github.com/phflot/flow_registration
properties (Constant) % SessionMethod attributes
BatchMode = 'serial' % Move to data method?
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/normcorre.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/normcorre.m
index d966b9063..23d9f4c2c 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/normcorre.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+motionCorrection/normcorre.m
@@ -1,6 +1,26 @@
classdef normcorre < nansen.session.SessionMethod & nansen.wrapper.normcorre.Processor
-%normcorre Summary of this function goes here
-% Detailed explanation goes here
+%Motion-correct the raw two-photon recording with NoRMCorre.
+%
+%Use this when:
+%- You want non-rigid motion correction using the NoRMCorre MATLAB toolbox.
+%- You need motion-corrected data plus diagnostic projections and movement
+% statistics saved back into the session.
+%
+%What happens:
+%- NANSEN loads `TwoPhotonSeries_Original` and enables stack preprocessing.
+%- NoRMCorre estimates frame shifts and writes the corrected stack.
+%- Reference images, projections, and correction statistics are generated
+% by the shared motion-correction pipeline.
+%
+%Outputs:
+%- `TwoPhotonSeries_Corrected`: motion-corrected image stack.
+%- `NormcorreOptions` and `NormcorreShifts`: method-specific settings and
+% frame shifts.
+%- Motion-correction QC outputs such as `FovAverageProjection`,
+% `FovMaximumProjection`, and `MotionCorrectionStats`.
+%
+%Reference:
+%- https://github.com/flatironinstitute/NoRMCorre
properties (Constant) % SessionMethod attributes
BatchMode = 'serial' % Move to data method?
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiClassifier.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiClassifier.m
index 515d274dc..bf62d51be 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiClassifier.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiClassifier.m
@@ -1,6 +1,21 @@
function varargout = openRoiClassifier(sessionObject, varargin)
-%OPENROICLASSIFIER Open roi classifier on a session
-% Detailed explanation goes here
+%Open the ROI classifier for a selected ROI variable.
+%
+%Use this when:
+%- You want to manually label ROIs as cells, non-cells, or other configured
+% classes.
+%- You have one or more ROI variables available for the selected session.
+%
+%What happens:
+%- NANSEN asks which ROI variable to classify.
+%- If needed, the ROI data are loaded through the ROI file adapter so the
+% classifier receives a roiGroup.
+%- If ROI images are missing, the motion-corrected stack is passed in so
+% the classifier can show image context.
+%
+%Outputs:
+%- Classification edits are handled by the ROI classifier app for the
+% selected ROI file.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -28,7 +43,7 @@
params = utility.parsenvpairs(params, 1, varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
sessionData = nansen.session.SessionData( sessionObject );
sessionData.updateDataVariables()
@@ -74,8 +89,7 @@
function S = getDefaultParameters()
S = struct();
- % Add more fields:
- S.RoiSelectedCallbackFunction = '';
+ S.RoiSelectedCallbackFunction = ''; % Optional callback used when an ROI is selected.
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiManager.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiManager.m
index c70280c8c..d4e2c3da2 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiManager.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiCuration/openRoiManager.m
@@ -1,6 +1,21 @@
function varargout = openRoiManager(sessionObj, varargin)
-%openRoimanager Open roimanager for corrected two-photon images
+%Open RoiManager for the motion-corrected two-photon recording.
%
+%Use this when:
+%- You want to inspect, draw, edit, or curate ROIs directly on the
+% motion-corrected image stack.
+%- You want to load an existing ROI variable into RoiManager for manual
+% correction.
+%
+%What happens:
+%- NANSEN loads `TwoPhotonSeries_Corrected` and enables dynamic caching for
+% interactive browsing.
+%- RoiManager opens on the corrected stack.
+%- If you choose an ROI variable, those ROIs are loaded into RoiManager and
+% linked to the current session data.
+%
+%Outputs:
+%- Edits are managed by RoiManager; this method itself only opens the app.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Please create a struct of default parameters (if applicable) and specify
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/classifyMultiSessionRois.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/classifyMultiSessionRois.m
index d66c38025..cae0156d6 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/classifyMultiSessionRois.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/classifyMultiSessionRois.m
@@ -1,6 +1,23 @@
function varargout = classifyMultiSessionRois(sessionObject, varargin)
-%CLASSIFYMULTISESSIONROIS Summary of this function goes here
-% Detailed explanation goes here
+%Classify matched ROIs across a longitudinal session set.
+%
+%Use this when:
+%- You have already migrated ROIs across sessions and computed
+% classification data for each session.
+%- You want one classifier view where corresponding ROIs from different
+% sessions stay aligned.
+%
+%What happens:
+%- NANSEN loads the multi-session ROI cross-reference from the first
+% selected session.
+%- `RoiGroupLongitudinal` data are loaded from each selected session and
+% reordered so matched ROIs appear together.
+%- The ROI classifier opens with session-aware labels.
+%- When classifications are saved, each session's `RoiGroupLongitudinal`
+% is updated with the new labels.
+%
+%Outputs:
+%- Updated `RoiGroupLongitudinal` files for the selected sessions.
% % % % % % % % % % % % % % % INSTRUCTIONS % % % % % % % % % % % % % % %
% - - - - - - - - - - You can remove this part - - - - - - - - - - -
@@ -43,7 +60,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
varName = 'MultisessionRoiCrossReference';
filePath = sessionObject(1).loadData(varName);
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/computeClassificationData.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/computeClassificationData.m
index 5c926d09d..fe78dd1b0 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/computeClassificationData.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/computeClassificationData.m
@@ -1,6 +1,22 @@
function varargout = computeClassificationData(sessionObject, varargin)
-%computeClassificationData Summary of this function goes here
-% Detailed explanation goes here
+%Compute ROI images and statistics for longitudinal ROI classification.
+%
+%Use this when:
+%- You have `RoiArrayLongitudinal` for a session and want to classify those
+% ROIs later.
+%- You need ROI thumbnails and ROI statistics derived from the
+% motion-corrected stack.
+%
+%What happens:
+%- NANSEN loads `RoiArrayLongitudinal` and the selected ImageStack.
+%- For each channel and plane, it computes ROI images and ROI statistics
+% from an initial chunk of frames.
+%- The ROI data, images, statistics, and empty classification labels are
+% packaged as a longitudinal ROI group.
+%
+%Outputs:
+%- `RoiGroupLongitudinal`: ROI data prepared for longitudinal
+% classification.
% % % % % % % % % % % % CONFIGURATION CODE BLOCK % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -104,16 +120,9 @@
end
function params = getDefaultParameters()
-%getDefaultParameters Get the default parameters for this session method
-%
-% params = getDefaultParameters() should return a struct, params, which
-% contains fields and values for parameters of this session method.
-
- % Add fields to this struct in order to define parameters for this
- % session method:
params = struct();
- params.ImageStackVariableName = 'TwoPhotonSeries_Corrected';
- params.RoiImageSize = [21, 21];
+ params.ImageStackVariableName = 'TwoPhotonSeries_Corrected'; % ImageStack used to compute ROI images and statistics.
+ params.RoiImageSize = [21, 21]; % Pixel size of generated ROI thumbnails.
end
function throwError(errorID, sessionID)
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/editRois.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/editRois.m
index c8236bcd7..d5ec2ff51 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/editRois.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/editRois.m
@@ -1,9 +1,21 @@
function varargout = editRois(sessionObject, varargin)
-%EDITROIS Edit rois for a set of longitudinal rois in roimanager.
-% This method opens the roimanager for editing rois for a set of
-% longitudinal sessions. It additionally opens a thumbnail selector for
-% switching between each of the sessions. If changes are made to rois in
-% one session, those changes will be copied to all other sessions.
+%Edit longitudinal ROIs across a selected session set.
+%
+%Use this when:
+%- You have migrated ROIs across sessions and want to manually correct the
+% matched ROI set.
+%- You need to switch between sessions while keeping RoiManager focused on
+% the corresponding longitudinal ROIs.
+%
+%What happens:
+%- NANSEN loads an FOV projection for each selected session.
+%- It loads `RoiArrayLongitudinal` and the selected ImageStack for each
+% session.
+%- RoiManager opens on the first session, together with a multi-session FOV
+% switcher for moving through the selected sessions.
+%
+%Outputs:
+%- ROI edits are managed by RoiManager and the multi-session switcher.
% Todo: Also support loading of roi classifications.
% Specify FOV image variable name in parameters.
@@ -75,15 +87,8 @@
end
function params = getDefaultParameters()
-%getDefaultParameters Get the default parameters for this session method
-%
-% params = getDefaultParameters() should return a struct, params, which
-% contains fields and values for parameters of this session method.
-
- % Add fields to this struct in order to define parameters for this
- % session method:
params = struct();
- params.ImageStackVariableName = 'TwoPhotonSeries_Corrected';
+ params.ImageStackVariableName = 'TwoPhotonSeries_Corrected'; % ImageStack shown in RoiManager.
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/migrateRoisToFovs.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/migrateRoisToFovs.m
index 0951c01b6..053aaf900 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/migrateRoisToFovs.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+roiRegistration/migrateRoisToFovs.m
@@ -1,25 +1,30 @@
function varargout = migrateRoisToFovs(sessionObject, varargin)
-%migrateRoisToFovs Summary of this function goes here
+%Migrate ROIs from one reference FOV to matching FOVs in other sessions.
%
-% This is a multisession method to use for migrating a roi array from one
-% FoV to other matching FOVs.
+%Use this when:
+%- You have repeated imaging sessions from matching fields of view.
+%- You want to start longitudinal ROI curation from one reference ROI set
+% instead of drawing ROIs independently in every session.
%
-% Requirements:
-% - - - - - - -
-% The method requires a FOV image ("FovAverageProjection") to be present
-% for all sessions and a roi array to be present for the reference session.
+%Requirements:
+%- Every selected session must have `FovAverageProjection` or
+% `FovAverageProjectionCorr`.
+%- The reference session must contain the ROI array you want to migrate.
+%- Multi-plane recordings are not supported by this method yet.
%
-% What will happen?
-% - - - - - - - - -
-% 1) An average FOV image is loaded for each session and aligned
-% using an image registration method (flowreg or normcorre).
-% 2) The roi array from the reference session will be copied to all other
-% sessions and the roi positions will be adjusted based on the pixel
-% shifts from the image registration step.
-% 3) Rois are added and saved to a MultiSessionRoiCollection. This can
-% later be used to manually edit rois for individual sessions and
-% synchronize those changes across all sessions. See
-% Roi Registration -> Edit Rois
+%What happens:
+%- You choose the reference session.
+%- FOV projections are loaded, aligned, and used to estimate pixel shifts
+% from the reference FOV to each target FOV.
+%- The reference ROI array is copied to each target session and shifted into
+% the aligned FOV coordinate frame.
+%- QC images are generated and opened so the migration can be inspected.
+%
+%Outputs:
+%- `RoiArrayLongitudinal`: migrated ROI arrays saved for each selected
+% session.
+%- `MultisessionRoiCrossReference`: path to the shared multi-session ROI
+% collection saved for each selected session.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -47,7 +52,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
% Count number of sessions
numSessions = numel(sessionObject);
@@ -251,12 +256,11 @@ function saveMultiSessionRois()
function S = getDefaultParameters()
S = struct();
- S.WorkingChannel = 2;
+ S.WorkingChannel = 2; % Imaging channel used for aligning FOVs and migrating ROIs.
S.WorkingChannel_ = {1,2};
% S.MultisessionRoiSynchMode ?
% 'LoadFromMaster', struct('Alternatives', {{'Use Master', 'Use Single', 'Merge'}}, 'Selection', {'Merge'}), ...
% 'SaveToMaster', struct('Alternatives', {{'Only Add', 'Mirror'}}, 'Selection', {'Mirror'}), ...
- % Add more fields:
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/SelectRoiForSignalExtraction.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/SelectRoiForSignalExtraction.m
index 03fdb6a8f..ba5ccb26d 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/SelectRoiForSignalExtraction.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/SelectRoiForSignalExtraction.m
@@ -1,18 +1,20 @@
function varargout = SelectRoiForSignalExtraction(sessionObject, varargin)
-%SELECTROIFORSIGNALEXTRACTION Select which rois to use for signal extraction
+%Choose which ROI set should be used for signal extraction.
%
-% This method updates the default ROI data variable for a Nansen session. It
-% prompts the user to select which ROI variable to work with. If a valid
-% variable name is chosen, the corresponding ROI group is retrieved and
-% saved to the default ROI variable.
+%Use this when:
+%- A session has multiple ROI variables, for example automatic detections
+% and manually curated ROIs.
+%- You want `Extract Signals` to use a specific ROI set.
%
-% Note: The default ROI variable is used for signal extraction
+%What happens:
+%- NANSEN asks which ROI variable to use.
+%- The selected ROI group can optionally be cleaned by removing ROIs with
+% pixels outside the FOV boundary.
+%- The selected ROI group is saved as the default `RoiArray`.
%
-% Parameters:
-% - deleteRoisOutsideTheBorders (logical) -
-% Boolean flag true, determining if ROIs whose pixels lie partially or
-% completely outside the field of view (FOV) boundaries are removed. The
-% updated ROI group is then saved back to the session.
+%Outputs:
+%- `RoiArray`: the ROI set that signal-extraction methods will use by
+% default.
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
% Create a struct of default parameters (if applicable) and specify one or
@@ -40,7 +42,7 @@
params = utility.parsenvpairs(params, [], varargin);
% % % % % % % % % % % % % % CUSTOM CODE BLOCK % % % % % % % % % % % % % %
-% Implementation of the method : Add your code here:
+% Implementation of the session method.
sessionData = nansen.session.SessionData( sessionObject );
sessionData.updateDataVariables()
@@ -86,6 +88,5 @@
function S = getDefaultParameters()
S = struct();
- % Add more fields:
- S.deleteRoisOutsideTheBorders = true;
+ S.deleteRoisOutsideTheBorders = true; % Remove ROIs with pixels outside the FOV before saving RoiArray.
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/computeDff.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/computeDff.m
index 152bfb259..07a5d812b 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/computeDff.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/computeDff.m
@@ -1,6 +1,21 @@
classdef computeDff < nansen.session.SessionMethod
-%COMPUTEDFF Summary of this function goes here
-% Detailed explanation goes here
+%Compute delta-F-over-F traces from extracted ROI signals.
+%
+%Use this when:
+%- You have already run signal extraction for the session.
+%- You want normalized ROI activity traces for visualization, deconvolution,
+% or downstream analysis.
+%
+%What happens:
+%- NANSEN loads `RoiSignals_MeanF`.
+%- If the selected dF/F method requires neuropil data, NANSEN also loads
+% `RoiSignals_NeuropilF`.
+%- The selected dF/F algorithm is applied to each ROI trace.
+%- Preview mode opens the dF/F explorer so parameters can be tuned before
+% committing the run.
+%
+%Outputs:
+%- `RoiSignals_Dff`: delta-F-over-F ROI signals.
properties (Constant) % SessionMethod attributes
MethodName = 'Compute Delta F over F'
@@ -30,7 +45,7 @@
methods (Static)
function options = getDefaultOptions()
- %GETDEFAULTOPTIONS Summary of this function goes here
+ %GETDEFAULTOPTIONS Return default delta-F-over-F options.
options = nansen.twophoton.roisignals.getDffParameters();
end
end
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignals.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignals.m
index ad5c55b43..621c738c0 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignals.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignals.m
@@ -1,6 +1,22 @@
classdef extractSignals < nansen.session.SessionMethod
-%EXTRACTSIGNALS Summary of this function goes here
-% Detailed explanation goes here
+%Extract fluorescence and neuropil signals from the corrected stack.
+%
+%Use this when:
+%- `TwoPhotonSeries_Corrected` and the default `RoiArray` are ready.
+%- You want per-ROI fluorescence traces before dF/F computation or
+% deconvolution.
+%
+%What happens:
+%- NANSEN loads the motion-corrected stack and the default ROI array.
+%- For each ROI, fluorescence is extracted from the ROI region and configured
+% neuropil regions.
+%- Signal metadata such as sample rate are inherited from the image stack
+% where available.
+%
+%Outputs:
+%- `RoiSignals_MeanF`: mean ROI fluorescence traces.
+%- `RoiSignals_NeuropilF`: neuropil fluorescence traces.
+%- `OptionsSignalExtraction`: options used for the extraction run.
properties (Constant) % SessionMethod attributes
MethodName = 'Extract Signals'
diff --git a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignalsMultiChannel.m b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignalsMultiChannel.m
index 9431110d1..8bc53868a 100644
--- a/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignalsMultiChannel.m
+++ b/code/modules/+nansen/+module/+ophys/+twophoton/+sessionmethod/+process/+signalExtraction/extractSignalsMultiChannel.m
@@ -1,8 +1,21 @@
classdef extractSignalsMultiChannel < nansen.session.SessionMethod
-%EXTRACTSIGNALS Summary of this function goes here
-% Detailed explanation goes here
+%Extract ROI signals from all channels in a multi-channel recording.
%
-% Session method wrapper for SignalExtractor
+%Use this when:
+%- `TwoPhotonSeries_Corrected` has multiple channels.
+%- The default `RoiArray` should be matched to the stack's channel and plane
+% layout before signal extraction.
+%
+%What happens:
+%- NANSEN loads the corrected stack and temporarily selects all channels.
+%- The ROI group is checked and adapted to match the stack dimensions.
+%- The `SignalExtractor` processor extracts ROI and neuropil signals using
+% the configured extraction options.
+%
+%Outputs:
+%- `RoiSignals_MeanF`: mean ROI fluorescence traces.
+%- `RoiSignals_NeuropilF`: neuropil fluorescence traces.
+%- `OptionsSignalExtraction`: options used by the signal extractor.
properties (Constant) % SessionMethod attributes
MethodName = 'Extract Signals (MultiChannel)'
diff --git a/code/resources/templates/helpwin.css b/code/resources/templates/helpwin.css
new file mode 100644
index 000000000..db4d6145a
--- /dev/null
+++ b/code/resources/templates/helpwin.css
@@ -0,0 +1,274 @@
+body {
+ font-family: 'Avenir Next', Helvetica, Arial, sans-serif;
+ font-size: 16px;
+ line-height: 1.55;
+ color: #303E4C;
+ background-color: #f7f8fb;
+ margin: 0;
+ padding: 0;
+}
+
+a {
+ color: #1F78B4;
+ text-decoration: none;
+ font-weight: 500;
+}
+
+a:visited {
+ color: #5C6F8C;
+}
+
+a:active {
+ color: #184A6D;
+}
+
+a:hover {
+ color: #0F3654;
+ text-decoration: underline;
+}
+
+hr {
+ border: none;
+ border-top: 2px solid #1F78B4;
+ margin: 30px 0;
+}
+
+p {
+ margin: 10px 0;
+ color: #404A59;
+ font-size: 16px;
+}
+
+code {
+ background-color: #EEF2F6;
+ border: 1px solid #DDE4EC;
+ border-radius: 3px;
+ color: #243746;
+ font-family: Menlo, Consolas, monospace;
+ font-size: 0.92em;
+ padding: 1px 4px;
+}
+
+table {
+ width: 100%;
+ border-collapse: collapse;
+ margin: 12px 0 22px;
+ font-size: 14px;
+ background-color: #fff;
+}
+
+table th,
+table td {
+ padding: 12px 15px;
+ text-align: left;
+ color: #303E4C;
+ border: none;
+}
+
+table th {
+ background-color: #E8EFF7;
+ font-weight: bold;
+ border-bottom: 2px solid #1F78B4;
+}
+
+table tr td {
+ border-bottom: 1px solid #E0E4EB;
+}
+
+table tr:nth-child(even) {
+ background-color: #F9FAFC;
+}
+
+table tbody tr:hover {
+ background-color: #E0E4EB !important; /* Ensure the hover color is applied */
+}
+
+.title {
+ color: #182633;
+ font-size: 30px;
+ font-weight: 700;
+ margin: 22px 0 8px;
+ border-bottom: 2px solid #D6DEE8;
+ padding-bottom: 10px;
+}
+
+.sectiontitle {
+ color: #184A6D;
+ font-size: 20px;
+ font-weight: 700;
+ margin: 28px 0 10px;
+}
+
+.headertitle {
+ font-weight: 700;
+ font-size: 13px;
+ letter-spacing: 0;
+ text-transform: uppercase;
+ color: #5F6F80;
+}
+
+.helptopic {
+ font-weight: bold;
+ color: #1F78B4;
+ font-size: 18px;
+ margin-top: 20px;
+}
+
+.helptext {
+ margin: 20px 0;
+ font-family: 'Avenir Next', Helvetica, Arial, sans-serif;
+ font-size: 17px;
+ line-height: 1.7;
+ color: #505F72;
+ background-color: #F2F5FA;
+ padding: 15px 20px;
+ border-left: 4px solid #1F78B4;
+ border-radius: 3px;
+}
+
+.method-page {
+ max-width: 980px;
+ margin: 0 auto;
+ padding: 22px 28px 36px;
+}
+
+.lead {
+ color: #344657;
+ font-size: 18px;
+ line-height: 1.55;
+ margin: 12px 0 20px;
+}
+
+.guide-text {
+ background-color: #FFFFFF;
+ border: 1px solid #DDE4EC;
+ border-radius: 6px;
+ padding: 18px 22px;
+}
+
+.guide-text h2 {
+ color: #184A6D;
+ font-size: 17px;
+ margin: 18px 0 8px;
+}
+
+.guide-text h2:first-child {
+ margin-top: 0;
+}
+
+.guide-text ul {
+ margin: 8px 0 14px 20px;
+ padding: 0;
+}
+
+.guide-text li {
+ margin: 5px 0;
+}
+
+.subheader {
+ border-bottom: 1px solid #DDE4EC;
+ padding-bottom: 10px;
+ color: #1F78B4;
+}
+
+.subheader-left {
+ float: left;
+ font-size: 18px;
+ font-weight: bold;
+}
+
+.subheader-right {
+ text-align: right;
+ float: right;
+ font-size: 18px;
+ font-weight: bold;
+}
+
+.footerlinktitle {
+ margin: 30px 0 10px;
+ color: #1F78B4;
+ font-size: 18px;
+ font-weight: bold;
+}
+
+.footerlink {
+ padding: 5px 10px;
+ color: #505F72;
+ display: inline-block;
+}
+
+.topiclinks {
+ margin: 20px 0;
+}
+
+a.topiclink {
+ padding-right: 15px;
+ color: #1F78B4;
+ font-weight: 500;
+}
+
+.class-details {
+ margin: 15px 20px;
+ padding: 15px;
+ background-color: #f2f5fa;
+ border-radius: 5px;
+ box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1);
+}
+
+.class-detail-label {
+ font-weight: bold;
+ padding-right: 10px;
+ color: #1F78B4;
+ font-size: 18px;
+}
+
+.name {
+ color: #184A6D;
+ font-weight: bold;
+ font-size: 18px;
+}
+
+.summary-list {
+ margin: 20px 0;
+ list-style: none;
+ padding: 0;
+}
+
+.summary-list .summary-item {
+ padding: 10px 12px;
+ margin-bottom: 6px;
+ background-color: #F9FAFC;
+ border-bottom: 1px solid #E0E4EB;
+}
+
+.summary-list .summary-item .name {
+ font-weight: bold;
+ color: #303E4C;
+ font-size: 14px;
+}
+
+.summary-list .summary-item .m-help {
+ font-size: 14px;
+ color: #505F72;
+ margin-top: 5px;
+}
+
+.summary-list .summary-item .attributes {
+ font-size: 14px;
+ text-align: center;
+ color: #1F78B4;
+ font-weight: 500;
+}
+
+.columntitle {
+ font-size: 14px;
+ font-weight: bold;
+ color: #303E4C;
+ padding: 8px 8px;
+ margin-bottom: 10px;
+}
+
+.empty-row .m-help {
+ color: #6B7887;
+ font-style: italic;
+}
diff --git a/code/resources/templates/session_method_help.html.template b/code/resources/templates/session_method_help.html.template
new file mode 100644
index 000000000..fb61d32de
--- /dev/null
+++ b/code/resources/templates/session_method_help.html.template
@@ -0,0 +1,51 @@
+
+
+
+
+
+ {{ title }}
+
+
+
+
+
+
NANSEN Session Method
+
+
{{ main_title }}
+
+ {{ helptext }}
+
+
+
Guide
+
+ {{ description }}
+
+
+
Option Presets
+
+ {% for preset in option_presets %}
+
+
{{ preset.name }}
+
{{ preset.description }}
+
+ {% endfor %}
+
+
+
Parameters
+
+
+
Name
+
Default value
+
Description
+
+
+
+
{{ param.name }}
+
{{ param.default_value }}
+
{{ param.description }}
+
+
+
+
+
+
diff --git a/code/wrappers/+nansen/+wrapper/+quicky/+presets/Axon.m b/code/wrappers/+nansen/+wrapper/+quicky/+presets/Axon.m
index 41107b7f4..69bf782d1 100644
--- a/code/wrappers/+nansen/+wrapper/+quicky/+presets/Axon.m
+++ b/code/wrappers/+nansen/+wrapper/+quicky/+presets/Axon.m
@@ -2,7 +2,7 @@
properties (Constant)
Name = 'Axons'
- Description = 'Autosegment neuronal axonal boutons'
+ Description = 'Tuned to detect smaller axonal bouton-like structures'
end
methods (Static)
diff --git a/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma.m b/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma.m
index 7922b8af4..986d1be59 100644
--- a/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma.m
+++ b/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma.m
@@ -2,7 +2,7 @@
properties (Constant)
Name = 'Soma'
- Description = 'Autosegment neuronal somas'
+ Description = 'Optimized for detecting soma-like structures'
end
methods (Static)
diff --git a/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma_Virus.m b/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma_Virus.m
index 7d947957f..ff5c2345b 100644
--- a/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma_Virus.m
+++ b/code/wrappers/+nansen/+wrapper/+quicky/+presets/Soma_Virus.m
@@ -2,7 +2,7 @@
properties (Constant)
Name = 'Soma (Virus)'
- Description = 'Autosegment neuronal somas'
+ Description = 'Optimized for viral GCaMP expression'
end
methods (Static)