flimkit 0.12.0__py3-none-any.whl

flimkit/UI/modes/fov_mode.py

@@ -0,0 +1,164 @@
+import tkinter as tk
+from tkinter import ttk
+
+from flimkit.UI.modes.base import BaseMode
+from flimkit.UI.utils import PAD, _C, _section, _row, _browse_file, _browse_dir, _tog, FLIM_FILETYPES
+from flimkit.UI.irf_widget import IRFWidget
+
+class FovMode(BaseMode):
+    def build(self):
+        outer, tab = self.b._form_inner_frames['fov']
+        tab.columnconfigure(0, weight=1)
+        ff = _section(tab, 'Input Files')
+        ff.grid(row=0, column=0, sticky='ew', pady=(0, 6))
+        ff.columnconfigure(0, weight=1)
+        atr = ttk.Frame(ff)
+        atr.grid(row=0, column=0, sticky='ew', pady=(0, 2))
+        ttk.Label(atr, text='Analysis:').pack(side='left', padx=(2, 8))
+        self.b.state.sv_fov_analysis = tk.StringVar(value='single')
+        ttk.Radiobutton(atr, text='Single FOV', variable=self.b.sv_fov_analysis,
+                        value='single', command=self.b._on_fov_analysis_changed).pack(side='left', padx=2)
+        ttk.Radiobutton(atr, text='Z-stack', variable=self.b.sv_fov_analysis,
+                        value='zstack', command=self.b._on_fov_analysis_changed).pack(side='left', padx=2)
+        ttk.Label(atr, text='(z-stack: a folder of region_zX.ptu slices, fitted as one FOV)',
+                  foreground='grey').pack(side='left', padx=(8, 0))
+        self.b.state.sv_ptu = tk.StringVar()
+        self.b.state.sv_xlsx = tk.StringVar()
+        self.b.state.sv_zstack_dir = tk.StringVar()
+        self.b.sv_ptu.trace_add('write', self.b._on_fov_ptu_changed)
+        self.b.sv_zstack_dir.trace_add('write', self.b._on_zstack_dir_changed)
+        single_fr = ttk.Frame(ff)
+        single_fr.grid(row=1, column=0, sticky='ew')
+        single_fr.columnconfigure(1, weight=1)
+        _row(single_fr, 'Data file *', self.b.sv_ptu, 0,
+             lambda: _browse_file(self.b.sv_ptu, 'FLIM file', FLIM_FILETYPES))
+        self.b._fov_single_fr = single_fr
+        zstack_fr = ttk.Frame(ff)
+        zstack_fr.grid(row=1, column=0, sticky='ew')
+        zstack_fr.columnconfigure(1, weight=1)
+        _row(zstack_fr, 'Z-stack folder *', self.b.sv_zstack_dir, 0,
+             lambda: _browse_dir(self.b.sv_zstack_dir,
+                                 'Folder of region_zX.ptu z-slices'))
+        self.b._fov_zstack_fr = zstack_fr
+        zstack_fr.grid_remove()
+        xlsx_fr = ttk.Frame(ff)
+        xlsx_fr.grid(row=2, column=0, sticky='ew')
+        xlsx_fr.columnconfigure(1, weight=1)
+        _row(xlsx_fr, 'LAS X export (optional)', self.b.sv_xlsx, 0,
+             lambda: _browse_file(self.b.sv_xlsx, 'LAS X export',
+                                  [('LAS X export', '*.xlsx *.csv *.tsv *.txt *.dat *.ascii *.asc'),
+                                   ('All', '*.*')]))
+        self.b._irf_fov = IRFWidget(tab, default='irf_xlsx', xlsx_var=self.b.sv_xlsx,
+                                   machine_irf_default=str(_C()['MACHINE_IRF_DEFAULT_PATH']))
+        self.b._irf_fov.grid(row=1, column=0, sticky='ew', pady=(0, 6))
+        fp = _section(tab, 'Fitting Parameters', help_topic='fit_model')
+        fp.grid(row=2, column=0, sticky='ew', pady=(0, 6))
+        ttk.Label(fp, text='Fit model:').grid(row=0, column=0, sticky='w', **PAD)
+        self.b.state.sv_fit_model_fov = tk.StringVar(value='discrete')
+        ttk.Radiobutton(fp, text='n-exp', variable=self.b.sv_fit_model_fov,
+                        value='discrete').grid(row=0, column=1, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='Gaussian dist.', variable=self.b.sv_fit_model_fov,
+                        value='gaussian').grid(row=0, column=2, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='Lorentzian dist.', variable=self.b.sv_fit_model_fov,
+                        value='lorentzian').grid(row=0, column=3, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='n-exp tail', variable=self.b.sv_fit_model_fov,
+                        value='tail').grid(row=0, column=4, sticky='w', padx=1)
+        self.b.state.iv_nexp_fov = tk.IntVar(value=2)
+        self.b.state.iv_ncomp_dist_fov = tk.IntVar(value=1)
+        nexp_frame = ttk.Frame(fp)
+        nexp_frame.grid(row=1, column=0, columnspan=5, sticky='w')
+        ttk.Label(nexp_frame, text='Components:').pack(side='left', padx=(4, 8))
+        for n in (1, 2, 3):
+            ttk.Radiobutton(nexp_frame, text=str(n), variable=self.b.iv_nexp_fov,
+                            value=n).pack(side='left', padx=1)
+        dist_frame = ttk.Frame(fp)
+        ttk.Label(dist_frame, text='Components:').pack(side='left', padx=(4, 8))
+        ttk.Radiobutton(dist_frame, text='1 (unimodal)', variable=self.b.iv_ncomp_dist_fov,
+                        value=1).pack(side='left', padx=1)
+        ttk.Radiobutton(dist_frame, text='2 (bimodal)', variable=self.b.iv_ncomp_dist_fov,
+                        value=2).pack(side='left', padx=1)
+        
+        tail_note = ttk.Label(fp, text='Tail fit: no IRF used, fitted past the decay peak',
+                              foreground='#888')
+        def _on_fov_model_change(*_):
+            _m = self.b.sv_fit_model_fov.get()
+            if _m in ('discrete', 'tail'):
+                dist_frame.grid_remove()
+                nexp_frame.grid(row=1, column=0, columnspan=5, sticky='w')
+            else:
+                nexp_frame.grid_remove()
+                dist_frame.grid(row=1, column=0, columnspan=5, sticky='w')
+            if _m == 'tail':
+                tail_note.grid(row=5, column=0, columnspan=5, sticky='w', padx=4)
+                self.b._irf_fov.grid_remove()
+            else:
+                tail_note.grid_remove()
+                self.b._irf_fov.grid(row=1, column=0, sticky='ew', pady=(0, 6))
+        self.b.sv_fit_model_fov.trace_add('write', _on_fov_model_change)
+        mode_row = ttk.Frame(fp)
+        mode_row.grid(row=2, column=0, columnspan=5, sticky='w', pady=(2, 0))
+        ttk.Label(mode_row, text='Fitting mode:').pack(side='left', padx=(0, 10))
+        self.b.state.sv_mode_fov = tk.StringVar(value='both')
+        radio_frame = ttk.Frame(mode_row)
+        radio_frame.pack(side='left')
+        ttk.Radiobutton(radio_frame, text='Full', variable=self.b.sv_mode_fov,
+                        value='both').pack(side='left', padx=2)
+        ttk.Radiobutton(radio_frame, text='Fast', variable=self.b.sv_mode_fov,
+                        value='summed').pack(side='left', padx=2)
+        ttk.Label(mode_row, text='(fast = no FLIM image)',
+                  foreground='grey').pack(side='left', padx=(10, 0))
+        ttk.Label(fp, text='Fit window (ns):').grid(row=3, column=0, sticky='w', **PAD)
+        self.b.state.sv_tau_min_fov = tk.StringVar(value=str(_C()['Tau_min']))
+        self.b.state.sv_tau_max_fov = tk.StringVar(value=str(_C()['Tau_max']))
+        ttk.Entry(fp, textvariable=self.b.sv_tau_min_fov, width=7).grid(row=3, column=1, sticky='w', padx=4)
+        ttk.Label(fp, text='to').grid(row=3, column=2)
+        ttk.Entry(fp, textvariable=self.b.sv_tau_max_fov, width=7).grid(row=3, column=3, sticky='w', padx=4)
+        ttk.Label(fp, text='ns  (fitting range)', foreground='grey').grid(row=3, column=4, sticky='w')
+        ttk.Label(fp, text='Output prefix:').grid(row=4, column=0, sticky='w', **PAD)
+        self.b.state.sv_out_fov = tk.StringVar(value='flim_out')
+        ttk.Entry(fp, textvariable=self.b.sv_out_fov, width=35).grid(
+            row=4, column=1, columnspan=3, sticky='ew', padx=4)
+        fm = _section(tab, 'Masking & Thresholding', help_topic='masking')
+        fm.grid(row=3, column=0, sticky='ew', pady=(0, 6))
+        self.b.state.bv_cell = tk.BooleanVar(value=False)
+        ttk.Checkbutton(fm, text='Apply cell mask (Cellpose-SAM)',
+                        variable=self.b.bv_cell).grid(
+            row=0, column=0, columnspan=3, sticky='w', **PAD)
+        self.b.state.bv_thr_fov = tk.BooleanVar(value=False)
+        self.b.state.sv_thr_fov = tk.StringVar()
+        ttk.Checkbutton(fm, text='Intensity threshold (min photons/px):',
+                        variable=self.b.bv_thr_fov,
+                        command=lambda: _tog(self.b.bv_thr_fov, self.b._thr_fov_e)).grid(
+            row=1, column=0, sticky='w', **PAD)
+        self.b._thr_fov_e = ttk.Entry(fm, textvariable=self.b.sv_thr_fov,
+                                    width=8, state='disabled')
+        self.b._thr_fov_e.grid(row=1, column=1, sticky='w', padx=4)
+        ttk.Label(fm, text='(leave blank for no threshold)',
+                  foreground='grey').grid(row=1, column=2, sticky='w')
+        self.b.state.bv_correct_pileup = tk.BooleanVar(value=False)
+        ttk.Checkbutton(fm, text='Apply Coates pile-up correction (recommended if pile-up > 5%)',
+                        variable=self.b.bv_correct_pileup).grid(
+            row=2, column=0, columnspan=3, sticky='w', **PAD)
+        ttk.Label(fm, text='Time-varying background PTU:').grid(row=3, column=0, sticky='w', **PAD)
+        self.b.state.sv_tvb_ptu_fov = tk.StringVar()
+        ttk.Entry(fm, textvariable=self.b.sv_tvb_ptu_fov, width=24).grid(
+            row=3, column=1, sticky='ew', padx=4)
+        ttk.Button(fm, text='Browse...',
+                   command=lambda: _browse_file(self.b.sv_tvb_ptu_fov,
+                                                'Background reference PTU',
+                                                FLIM_FILETYPES)).grid(
+            row=3, column=2, sticky='w', padx=4)
+        ttk.Label(fm, text='(optional: fits a measured fluorophore-free background decay, FLIMfit-style)',
+                  foreground='grey').grid(row=4, column=0, columnspan=3, sticky='w', padx=8)
+        self.b._expert_banner_fov = ttk.Label(
+            tab, text='⚙  Custom expert settings active',
+            foreground='#e8a838', font=('TkDefaultFont', 9, 'bold'))
+        self.b._expert_banner_fov.grid(row=4, column=0, sticky='w', padx=8)
+        self.b._expert_banner_fov.grid_remove()
+        btn_row_fov = ttk.Frame(tab)
+        btn_row_fov.grid(row=5, column=0, pady=8)
+        ttk.Button(btn_row_fov, text='⚙  Expert Settings',
+                   command=self.b._open_expert_settings).pack(side='left', padx=4)
+        self.b._btn_fov = ttk.Button(btn_row_fov, text='▶  Run Single-FOV Fit',
+                                   command=self.b._run_fov)
+        self.b._btn_fov.pack(side='left', padx=4, ipadx=20, ipady=4)

flimkit/UI/modes/irf_mode.py

@@ -0,0 +1,80 @@
+import tkinter as tk
+from tkinter import ttk
+
+from flimkit.UI.modes.base import BaseMode
+from flimkit.UI.utils import PAD, _C, _section, _row, _browse_dir
+
+
+class IrfMode(BaseMode):
+    def build(self):
+        outer, tab = self.b._form_inner_frames['irf']
+        tab.columnconfigure(0, weight=1)
+
+        cfg = _C()
+
+        ff = _section(tab, 'Source Data')
+        ff.grid(row=0, column=0, sticky='ew', pady=(0, 6))
+        ff.columnconfigure(1, weight=1)
+        self.b.state.sv_mirf_src = tk.StringVar()
+        _row(
+            ff,
+            'PTU/XLSX folder *',
+            self.b.sv_mirf_src,
+            0,
+            lambda: _browse_dir(self.b.sv_mirf_src, 'Folder with paired .ptu and .xlsx'),
+        )
+        ttk.Label(
+            ff,
+            text='Builder uses matching <name>.ptu + <name>.xlsx pairs.',
+            foreground='grey',
+        ).grid(row=1, column=1, columnspan=2, sticky='w', padx=4)
+
+        fp = _section(tab, 'Build Settings')
+        fp.grid(row=1, column=0, sticky='ew', pady=(0, 6))
+        fp.columnconfigure(1, weight=1)
+
+        self.b.state.sv_mirf_anchor = tk.StringVar(value=cfg['MACHINE_IRF_ALIGN_ANCHOR'])
+        self.b.state.sv_mirf_reducer = tk.StringVar(value=cfg['MACHINE_IRF_REDUCER'])
+
+        ttk.Label(fp, text='Align anchor:').grid(row=0, column=0, sticky='w', **PAD)
+        ttk.Combobox(
+            fp,
+            textvariable=self.b.sv_mirf_anchor,
+            values=['peak', 'halfmax', 'onset10', 'slope'],
+            state='readonly',
+            width=12,
+        ).grid(row=0, column=1, sticky='w', padx=4)
+
+        ttk.Label(fp, text='Reducer:').grid(row=1, column=0, sticky='w', **PAD)
+        ttk.Combobox(
+            fp,
+            textvariable=self.b.sv_mirf_reducer,
+            values=['median', 'mean'],
+            state='readonly',
+            width=12,
+        ).grid(row=1, column=1, sticky='w', padx=4)
+
+        fo = _section(tab, 'Output')
+        fo.grid(row=2, column=0, sticky='ew', pady=(0, 6))
+        fo.columnconfigure(1, weight=1)
+        self.b.state.sv_mirf_out_dir = tk.StringVar(value=str(cfg['MACHINE_IRF_DIR']))
+        self.b.state.sv_mirf_name = tk.StringVar(value='machine_irf_default')
+
+        _row(
+            fo,
+            'Output directory *',
+            self.b.sv_mirf_out_dir,
+            0,
+            lambda: _browse_dir(self.b.sv_mirf_out_dir, 'Machine IRF output directory'),
+        )
+        ttk.Label(fo, text='Base filename:').grid(row=1, column=0, sticky='w', **PAD)
+        ttk.Entry(fo, textvariable=self.b.sv_mirf_name, width=35).grid(
+            row=1, column=1, columnspan=2, sticky='ew', padx=4
+        )
+
+        self.b._btn_mirf = ttk.Button(
+            tab,
+            text='▶  Build Machine IRF',
+            command=self.b._run_build_machine_irf,
+        )
+        self.b._btn_mirf.grid(row=3, column=0, pady=8, ipadx=20, ipady=4)

flimkit/UI/modes/phasor_mode.py

@@ -0,0 +1,131 @@
+import tkinter as tk
+from tkinter import ttk
+
+from flimkit.UI.modes.base import BaseMode
+from flimkit.UI.utils import PAD, _C, _section, _row, _browse_file, FLIM_FILETYPES
+from flimkit.UI.phasor_panel import PhasorViewPanel
+
+
+class PhasorMode(BaseMode):
+    def build(self):
+        outer, inner = self.b._form_inner_frames['phasor']
+        inner.columnconfigure(0, weight=1)
+        ctrl = ttk.Frame(inner, padding=(6, 4))
+        ctrl.grid(row=0, column=0, sticky='ew')
+        ctrl.columnconfigure(0, weight=1)
+
+        mode_fr = _section(ctrl, 'Input Mode')
+        mode_fr.grid(row=0, column=0, sticky='ew', pady=(0, 4))
+        mode_fr.columnconfigure(1, weight=1)
+
+        self.b.state.sv_ph_mode = tk.StringVar(value='new')
+        ttk.Radiobutton(mode_fr, text='New PTU file',
+                        variable=self.b.sv_ph_mode, value='new',
+                        command=self.b._ph_mode_changed).grid(
+            row=0, column=0, sticky='w', padx=4, pady=1)
+        ttk.Radiobutton(mode_fr, text='Resume session (.npz)',
+                        variable=self.b.sv_ph_mode, value='session',
+                        command=self.b._ph_mode_changed).grid(
+            row=0, column=1, sticky='w', padx=4, pady=1)
+
+        self.b._ph_new = ttk.Frame(ctrl)
+        self.b._ph_new.columnconfigure(0, weight=1)
+        self.b._ph_new.grid(row=1, column=0, sticky='ew')
+        fn = _section(self.b._ph_new, 'New Analysis')
+        fn.grid(row=0, column=0, sticky='ew')
+        fn.columnconfigure(1, weight=1)
+        self.b.state.sv_ph_ptu  = tk.StringVar()
+        self.b.state.sv_ph_irf  = tk.StringVar()
+        self.b.state.sv_ph_mirf = tk.StringVar(
+            value=str(_C()['MACHINE_IRF_DEFAULT_PATH']))
+        _row(fn, 'PTU file *',             self.b.sv_ph_ptu,  0,
+             lambda: _browse_file(self.b.sv_ph_ptu, 'PTU file',
+                                  FLIM_FILETYPES))
+        _row(fn, 'IRF XLSX (optional)',    self.b.sv_ph_irf,  1,
+             lambda: _browse_file(self.b.sv_ph_irf, 'IRF XLSX',
+                                  [('Excel', '*.xlsx'), ('All', '*.*')]))
+        _row(fn, 'Machine IRF (optional)', self.b.sv_ph_mirf, 2,
+             lambda: _browse_file(self.b.sv_ph_mirf, 'Machine IRF',
+                                  [('NumPy', '*.npy'), ('All', '*.*')]))
+        ttk.Label(fn, text='XLSX takes priority if both supplied',
+                  foreground='grey').grid(
+            row=3, column=1, columnspan=2, sticky='w', padx=4)
+
+        self.b._ph_sess = ttk.Frame(ctrl)
+        self.b._ph_sess.columnconfigure(0, weight=1)
+        self.b._ph_sess.grid(row=2, column=0, sticky='ew')
+        fs = _section(self.b._ph_sess, 'Resume Session')
+        fs.grid(row=0, column=0, sticky='ew')
+        fs.columnconfigure(1, weight=1)
+        self.b.state.sv_ph_session = tk.StringVar()
+        _row(fs, 'Session (.npz) *', self.b.sv_ph_session, 0,
+             lambda: _browse_file(self.b.sv_ph_session, 'Session file',
+                                  [('NPZ', '*.npz'), ('All', '*.*')]))
+        self.b._ph_sess.grid_remove()
+
+        opt_fr = _section(ctrl, 'Display Options')
+        opt_fr.grid(row=3, column=0, sticky='ew', pady=(4, 0))
+        ttk.Label(opt_fr, text='Min photons (fraction):').grid(
+            row=0, column=0, sticky='w', **PAD)
+        self.b.state.sv_ph_minph = tk.StringVar(value='0.01')
+        ttk.Entry(opt_fr, textvariable=self.b.sv_ph_minph, width=8).grid(
+            row=0, column=1, sticky='w', padx=4)
+        ttk.Label(opt_fr, text='Max cursors:').grid(
+            row=0, column=2, sticky='w', padx=8)
+        self.b.state.sv_ph_maxc = tk.StringVar(value='6')
+        ttk.Entry(opt_fr, textvariable=self.b.sv_ph_maxc, width=4).grid(
+            row=0, column=3, sticky='w', padx=4)
+
+        self.b._btn_ph = ttk.Button(ctrl, text='▶  Load & Analyse',
+                                   command=self.b._run_phasor)
+        self.b._btn_ph.grid(row=4, column=0, pady=(6, 2), ipadx=16, ipady=3,
+                          sticky='w')
+
+        peaks_fr = _section(ctrl, 'Find Peaks')
+        peaks_fr.grid(row=5, column=0, sticky='ew', pady=(6, 0))
+        peaks_fr.columnconfigure(1, weight=1)
+        ttk.Label(peaks_fr, text='Smooth σ:').grid(
+            row=0, column=0, sticky='w', **PAD)
+        self.b.state.sv_ph_pk_sigma = tk.StringVar(value='3.0')
+        ttk.Entry(peaks_fr, textvariable=self.b.sv_ph_pk_sigma, width=6).grid(
+            row=0, column=1, sticky='w', padx=4)
+        ttk.Label(peaks_fr, text='Threshold:').grid(
+            row=1, column=0, sticky='w', **PAD)
+        self.b.state.sv_ph_pk_thresh = tk.StringVar(value='0.10')
+        ttk.Entry(peaks_fr, textvariable=self.b.sv_ph_pk_thresh, width=6).grid(
+            row=1, column=1, sticky='w', padx=4)
+        ttk.Button(peaks_fr, text='🔍  Find Peaks',
+                   command=self.b._run_ph_find_peaks).grid(
+            row=2, column=0, columnspan=2, sticky='w', pady=(4, 0), padx=8)
+
+        fret_fr = _section(ctrl, 'FRET Analysis')
+        fret_fr.grid(row=6, column=0, sticky='ew', pady=(6, 0))
+        fret_fr.columnconfigure(1, weight=1)
+        ttk.Label(fret_fr, text='Donor τ (ns):').grid(
+            row=0, column=0, sticky='w', **PAD)
+        self.b.state.sv_ph_fret_taud = tk.StringVar(value='4.0')
+        ttk.Entry(fret_fr, textvariable=self.b.sv_ph_fret_taud, width=8).grid(
+            row=0, column=1, sticky='w', padx=4)
+        ttk.Label(fret_fr, text='Acceptor τ (ns):').grid(
+            row=1, column=0, sticky='w', **PAD)
+        self.b.state.sv_ph_fret_taua = tk.StringVar(value='')
+        ttk.Entry(fret_fr, textvariable=self.b.sv_ph_fret_taua, width=8).grid(
+            row=1, column=1, sticky='w', padx=4)
+        ttk.Label(fret_fr, text='(blank = donor-only)',
+                  foreground='grey').grid(
+            row=1, column=2, sticky='w', padx=2)
+        ttk.Label(fret_fr, text='Donor fretting:').grid(
+            row=2, column=0, sticky='w', **PAD)
+        self.b.state.sv_ph_fret_fretting = tk.StringVar(value='1.0')
+        ttk.Entry(fret_fr, textvariable=self.b.sv_ph_fret_fretting, width=8).grid(
+            row=2, column=1, sticky='w', padx=4)
+        _fret_btn_fr = ttk.Frame(fret_fr)
+        _fret_btn_fr.grid(row=3, column=0, columnspan=3,
+                          sticky='w', pady=(4, 0), padx=8)
+        ttk.Button(_fret_btn_fr, text='↔  Overlay Trajectory',
+                   command=self.b._run_ph_fret_overlay).pack(side='left', padx=(0, 4))
+        ttk.Button(_fret_btn_fr, text='Fit Donor FRET',
+                   command=self.b._run_ph_fit_fret).pack(side='left', padx=(0, 4))
+        ttk.Button(_fret_btn_fr, text='✕  Clear Overlay',
+                   command=lambda: self.b._phasor_panel.clear_fret_overlay()).pack(
+            side='left')

flimkit/UI/modes/stitch_mode.py

@@ -0,0 +1,254 @@
+import tkinter as tk
+from tkinter import ttk
+
+from flimkit.UI.modes.base import BaseMode
+from flimkit.UI.utils import PAD, _C, _section, _row, _browse_file, _browse_dir, _tog, FLIM_FILETYPES
+from flimkit.UI.irf_widget import IRFWidget
+
+
+class StitchMode(BaseMode):
+    def build(self):
+        outer, tab = self.b._form_inner_frames['stitch']
+        tab.columnconfigure(0, weight=1)
+
+        ff = _section(tab, 'Input Files')
+        ff.grid(row=0, column=0, sticky='ew', pady=(0, 6))
+        ff.columnconfigure(1, weight=1)
+        self.b.state.sv_xlif = tk.StringVar()
+        self.b.sv_xlif.trace_add('write', self.b._on_xlif_changed)
+        self.b.state.sv_ptu_dir = tk.StringVar()
+        self.b.state.sv_out_st = tk.StringVar()
+
+        _row(ff, 'XLIF metadata *',      self.b.sv_xlif,    0,
+             lambda: _browse_file(self.b.sv_xlif, 'XLIF file',
+                                  [('XLIF', '*.xlif'), ('All', '*.*')]))
+        _row(ff, 'PTU tile directory *', self.b.sv_ptu_dir, 1,
+             lambda: _browse_dir(self.b.sv_ptu_dir, 'PTU tile directory'))
+        _row(ff, 'Base output dir *',    self.b.sv_out_st,  2,
+             lambda: _browse_dir(self.b.sv_out_st, 'Output directory'))
+
+        ttk.Label(ff, text='(A sub-folder named after the ROI will be created inside)',
+                  foreground='grey').grid(row=3, column=1, columnspan=2,
+                                         sticky='w', padx=4)
+        self.b.state.bv_rotate = tk.BooleanVar(value=True)
+        ttk.Checkbutton(ff, text='Rotate tiles 90° CW (recommended for FLIM microscope)',
+                        variable=self.b.bv_rotate).grid(
+            row=4, column=0, columnspan=3, sticky='w', padx=4, pady=(4, 0))
+
+        fp = _section(tab, 'Pipeline')
+        fp.grid(row=1, column=0, sticky='ew', pady=(4, 2))
+        self.b.state.sv_pipeline = tk.StringVar(value='stitch_only')
+        for r, (val, lbl) in enumerate([
+            ('stitch_only', 'Stitch tiles only'),
+            ('stitch_fit', 'Stitch then fit full ROI'),
+            ('tile_fit', 'Per-tile fit  [recommended - fits each tile independently]'),
+            ('series_fit', 'Multidimensional series  [z-stack and/or timelapse tiles]'),
+        ]):
+            ttk.Radiobutton(fp, text=lbl, variable=self.b.sv_pipeline,
+                            value=val, command=self.b._pipeline_changed).grid(
+                row=r, column=0, sticky='w', padx=4, pady=1)
+
+        self.b._fit_frame = ttk.Frame(tab)
+        self.b._fit_frame.columnconfigure(0, weight=1)
+        self.b._fit_frame.grid(row=2, column=0, sticky='ew')
+        self.build_fit(self.b._fit_frame)
+        self.b._fit_frame.grid_remove()
+
+        self.b._expert_banner_st = ttk.Label(
+            tab, text='⚙  Custom expert settings active',
+            foreground='#e8a838', font=('TkDefaultFont', 9, 'bold'))
+        self.b._expert_banner_st.grid(row=3, column=0, sticky='w', padx=8)
+        self.b._expert_banner_st.grid_remove()
+
+        btn_row_st = ttk.Frame(tab)
+        btn_row_st.grid(row=4, column=0, pady=8)
+        self.b._btn_expert_st = ttk.Button(btn_row_st, text='⚙  Expert Settings',
+                   command=self.b._open_expert_settings)
+        self.b._btn_expert_st.pack(side='left', padx=4)
+        self.b._btn_st = ttk.Button(btn_row_st, text='▶  Run Tile Stitch',
+                                  command=self.b._run_stitch)
+        self.b._btn_st.pack(side='left', padx=4, ipadx=20, ipady=4)
+
+    def build_fit(self, parent):
+        self.b._irf_st = IRFWidget(parent, default='machine_irf',
+                                  machine_irf_default=str(_C()['MACHINE_IRF_DEFAULT_PATH']))
+        self.b._irf_st.grid(row=0, column=0, sticky='ew', pady=(0, 6))
+        self.b._irf_st.frame.columnconfigure(1, weight=1)
+
+        fp = _section(parent, 'Fitting Parameters', help_topic='fit_model')
+        fp.grid(row=1, column=0, sticky='ew', pady=(0, 6))
+
+        ttk.Label(fp, text='Fit model:').grid(row=0, column=0, sticky='w', **PAD)
+        self.b.state.sv_fit_model_st = tk.StringVar(value='discrete')
+        ttk.Radiobutton(fp, text='n-exp', variable=self.b.sv_fit_model_st,
+                        value='discrete').grid(row=0, column=1, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='Gaussian dist.', variable=self.b.sv_fit_model_st,
+                        value='gaussian').grid(row=0, column=2, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='Lorentzian dist.', variable=self.b.sv_fit_model_st,
+                        value='lorentzian').grid(row=0, column=3, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='n-exp tail', variable=self.b.sv_fit_model_st,
+                        value='tail').grid(row=0, column=4, sticky='w', padx=1)
+
+        self.b.state.iv_nexp_st = tk.IntVar(value=2)
+        self.b.state.iv_ncomp_dist_st = tk.IntVar(value=1)
+
+        nexp_frame_st = ttk.Frame(fp)
+        nexp_frame_st.grid(row=1, column=0, columnspan=5, sticky='w')
+        ttk.Label(nexp_frame_st, text='Components:').pack(side='left', padx=(4, 8))
+        for n in (1, 2, 3):
+            ttk.Radiobutton(nexp_frame_st, text=str(n), variable=self.b.iv_nexp_st,
+                            value=n).pack(side='left', padx=4)
+
+        dist_frame_st = ttk.Frame(fp)
+        ttk.Label(dist_frame_st, text='Components:').pack(side='left', padx=(4, 8))
+        ttk.Radiobutton(dist_frame_st, text='1 (unimodal)', variable=self.b.iv_ncomp_dist_st,
+                        value=1).pack(side='left', padx=4)
+        ttk.Radiobutton(dist_frame_st, text='2 (bimodal)', variable=self.b.iv_ncomp_dist_st,
+                        value=2).pack(side='left', padx=4)
+
+        tail_note_st = ttk.Label(fp, text='Tail fit: no IRF used, fitted past the decay peak',
+                                 foreground='#888')
+        def _on_st_model_change(*_):
+            _m = self.b.sv_fit_model_st.get()
+            if _m in ('discrete', 'tail'):
+                dist_frame_st.grid_remove()
+                nexp_frame_st.grid(row=1, column=0, columnspan=5, sticky='w')
+            else:
+                nexp_frame_st.grid_remove()
+                dist_frame_st.grid(row=1, column=0, columnspan=5, sticky='w')
+            if _m == 'tail':
+                tail_note_st.grid(row=6, column=0, columnspan=5, sticky='w', padx=4)
+                self.b._irf_st.grid_remove()
+            else:
+                tail_note_st.grid_remove()
+                self.b._irf_st.grid(row=0, column=0, sticky='ew', pady=(0, 6))
+        self.b.sv_fit_model_st.trace_add('write', _on_st_model_change)
+
+        self.b.state.bv_perpix = tk.BooleanVar(value=False)
+        ttk.Checkbutton(fp, text='Per-pixel fitting [REQUIRED FOR ROI ANALYSIS]',
+                        variable=self.b.bv_perpix,
+                        command=self.b._perpix_toggled).grid(
+            row=2, column=0, columnspan=4, sticky='w', **PAD)
+
+        self.b._pxf = ttk.Frame(fp)
+        self.b._pxf.grid(row=3, column=0, columnspan=4, sticky='ew', padx=20)
+
+        self.b.state.bv_save_tau_weighted = tk.BooleanVar(value=True)
+        self.b.state.bv_save_int_weighted = tk.BooleanVar(value=True)
+        self.b.state.bv_save_amp_weighted = tk.BooleanVar(value=False)
+        self.b.state.bv_save_ind = tk.BooleanVar(value=False)
+
+        ttk.Checkbutton(self.b._pxf, text='Export τ-weighted map',
+                        variable=self.b.bv_save_tau_weighted).grid(row=0, column=0, sticky='w', padx=(0, 8))
+        ttk.Checkbutton(self.b._pxf, text='Export intensity-weighted map',
+                        variable=self.b.bv_save_int_weighted).grid(row=0, column=1, sticky='w', padx=(0, 8))
+        ttk.Checkbutton(self.b._pxf, text='Export amplitude-weighted map',
+                        variable=self.b.bv_save_amp_weighted).grid(row=1, column=0, sticky='w', padx=(0, 8))
+        ttk.Checkbutton(self.b._pxf, text='Save individual component maps',
+                        variable=self.b.bv_save_ind).grid(row=1, column=1, sticky='w')
+
+        self.b.state.sv_tau_lo = tk.StringVar()
+        self.b.state.sv_tau_hi = tk.StringVar()
+        self.b.state.sv_int_lo = tk.StringVar()
+        self.b.state.sv_int_hi = tk.StringVar()
+
+        ttk.Label(self.b._pxf, text='Lifetime display (ns):').grid(row=2, column=0, sticky='w', pady=2)
+        ttk.Entry(self.b._pxf, textvariable=self.b.sv_tau_lo, width=7).grid(row=2, column=1, padx=4)
+        ttk.Label(self.b._pxf, text='to').grid(row=2, column=2)
+        ttk.Entry(self.b._pxf, textvariable=self.b.sv_tau_hi, width=7).grid(row=2, column=3, padx=4)
+        ttk.Label(self.b._pxf, text='(blank = auto)', foreground='grey').grid(row=2, column=4, padx=4)
+
+        ttk.Label(self.b._pxf, text='Intensity display:').grid(row=3, column=0, sticky='w', pady=2)
+        ttk.Entry(self.b._pxf, textvariable=self.b.sv_int_lo, width=7).grid(row=3, column=1, padx=4)
+        ttk.Label(self.b._pxf, text='to').grid(row=3, column=2)
+        ttk.Entry(self.b._pxf, textvariable=self.b.sv_int_hi, width=7).grid(row=3, column=3, padx=4)
+        ttk.Label(self.b._pxf, text='(blank = auto)', foreground='grey').grid(row=3, column=4, padx=4)
+
+        self.b._pxf.grid_remove()
+
+        self.b.state.sv_tau_fit_lo = tk.StringVar(value=str(_C()['Tau_min']))
+        self.b.state.sv_tau_fit_hi = tk.StringVar(value=str(_C()['Tau_max']))
+        ttk.Label(fp, text='Fit window (ns):').grid(row=3, column=0, sticky='w', pady=2)
+        ttk.Entry(fp, textvariable=self.b.sv_tau_fit_lo, width=7).grid(row=3, column=1, padx=4)
+        ttk.Label(fp, text='to').grid(row=3, column=2)
+        ttk.Entry(fp, textvariable=self.b.sv_tau_fit_hi, width=7).grid(row=3, column=3, padx=4)
+        ttk.Label(fp, text='ns  (fitting range)', foreground='grey').grid(row=3, column=4, padx=4)
+
+        fm = _section(parent, 'Masking & Thresholding', help_topic='masking')
+        fm.grid(row=2, column=0, sticky='ew', pady=(0, 6))
+
+        self.b.state.bv_thr_st = tk.BooleanVar(value=False)
+        self.b.state.sv_thr_st = tk.StringVar()
+        ttk.Checkbutton(fm, text='Intensity threshold (min photons/px):',
+                        variable=self.b.bv_thr_st,
+                        command=lambda: _tog(self.b.bv_thr_st, self.b._thr_st_e)).grid(
+            row=0, column=0, sticky='w', **PAD)
+        self.b._thr_st_e = ttk.Entry(fm, textvariable=self.b.sv_thr_st,
+                                   width=8, state='disabled')
+        self.b._thr_st_e.grid(row=0, column=1, sticky='w', padx=4)
+        ttk.Label(fm, text='(leave blank for no threshold)',
+                  foreground='grey').grid(row=0, column=2, sticky='w')
+
+        self.b.state.bv_correct_pileup_st = tk.BooleanVar(value=False)
+        ttk.Checkbutton(fm, text='Apply Coates pile-up correction (recommended if pile-up > 5%)',
+                        variable=self.b.bv_correct_pileup_st).grid(
+            row=1, column=0, columnspan=3, sticky='w', **PAD)
+        ttk.Label(fm, text='Time-varying background PTU:').grid(row=2, column=0, sticky='w', **PAD)
+        self.b.state.sv_tvb_ptu_st = tk.StringVar()
+        ttk.Entry(fm, textvariable=self.b.sv_tvb_ptu_st, width=24).grid(
+            row=2, column=1, sticky='ew', padx=4)
+        ttk.Button(fm, text='Browse...',
+                   command=lambda: _browse_file(self.b.sv_tvb_ptu_st,
+                                                'Background reference PTU',
+                                                FLIM_FILETYPES)).grid(
+            row=2, column=2, sticky='w', padx=4)
+        ttk.Label(fm, text='(optional: measured background, aligned per tile)',
+                  foreground='grey').grid(row=3, column=0, columnspan=3, sticky='w', padx=8)
+        freg = _section(parent, 'Tile Registration')
+        freg.grid(row=3, column=0, sticky='ew', pady=(0, 6))
+        self.b.state.bv_register = tk.BooleanVar(value=True)
+        ttk.Checkbutton(freg, text='Phase-correlation registration (fixes stage Y/X drift)',
+                        variable=self.b.bv_register).grid(
+            row=0, column=0, columnspan=3, sticky='w', **PAD)
+        ttk.Label(freg, text='Max shift (px):').grid(row=1, column=0, sticky='w', **PAD)
+        self.b.state.sv_reg_max_shift = tk.StringVar(value='120')
+        ttk.Entry(freg, textvariable=self.b.sv_reg_max_shift, width=6).grid(
+            row=1, column=1, sticky='w', padx=4)
+        ttk.Label(freg, text='(increase if drift > 120px)',
+                  foreground='grey').grid(row=1, column=2, sticky='w')
+
+        self.b._series_frame = ttk.Frame(parent)
+        self.b._series_frame.columnconfigure(0, weight=1)
+        self.b._series_frame.grid(row=5, column=0, sticky='ew', pady=(0, 4))
+        fsr = _section(self.b._series_frame, 'Multidimensional Series')
+        fsr.grid(row=0, column=0, sticky='ew')
+        ttk.Label(fsr, text='Pool decay every N timepoints:').grid(
+            row=0, column=0, sticky='w', **PAD)
+        self.b.state.sv_pool_stride = tk.StringVar(value='10')
+        ttk.Entry(fsr, textvariable=self.b.sv_pool_stride, width=6).grid(
+            row=0, column=1, sticky='w', padx=4)
+        ttk.Label(fsr, text='(1 = every timepoint; higher is faster, same consensus)',
+                  foreground='grey').grid(row=0, column=2, sticky='w')
+        ttk.Label(fsr, text='One consensus lifetime is fitted across the whole series, '
+                            'so amplitudes stay comparable between timepoints.',
+                  foreground='grey', wraplength=520, justify='left').grid(
+            row=1, column=0, columnspan=3, sticky='w', padx=8, pady=(2, 0))
+        ttk.Label(fsr, text='An XLIF or LIF is used as the starting layout and then refined '
+                            'against the tile overlap. Without one the positions come from '
+                            'the overlap alone, which is less reliable on sparse samples.',
+                  foreground='grey', wraplength=520, justify='left').grid(
+            row=2, column=0, columnspan=3, sticky='w', padx=8)
+        self.b._series_frame.grid_remove()
+
+        self.b._tile_extras_frame = ttk.Frame(parent)
+        self.b._tile_extras_frame.columnconfigure(0, weight=1)
+        self.b._tile_extras_frame.grid(row=4, column=0, sticky='ew', pady=(0, 4))
+        fte = _section(self.b._tile_extras_frame, 'Per-Tile IRF Directory (optional)')
+        fte.grid(row=0, column=0, sticky='ew')
+        fte.columnconfigure(1, weight=1)
+        self.b.state.sv_tile_irf_dir = tk.StringVar()
+        _row(fte, 'IRF XLSX dir', self.b.sv_tile_irf_dir, 0,
+             lambda: _browse_dir(self.b.sv_tile_irf_dir, 'Directory of per-tile IRF xlsx files'))
+        ttk.Label(fte, text='One <tile_name>.xlsx per tile; leave blank to use IRF method above',
+                  foreground='grey').grid(row=1, column=1, columnspan=2, sticky='w', padx=4)
+        self.b._tile_extras_frame.grid_remove()