flimkit 0.12.0__py3-none-any.whl

flimkit/UI/irf_widget.py

@@ -0,0 +1,103 @@
+from __future__ import annotations
+import tkinter as tk
+from tkinter import ttk
+from typing import Optional
+from flimkit.UI.utils import _browse_file, _section
+class IRFWidget:
+    _AUTO_FILL = object()
+    CHOICES = [
+        ('Analytical model (LAS X export)',              'irf_xlsx'),
+        ('Machine IRF (.npy pre-built)',                 'machine_irf'),
+        ('Machine IRF + full σ broadening',               'machine_irf_sigma_full'),
+        ('Machine IRF + half σ broadening (σ≤0.5)',       'machine_irf_sigma_half'),
+        ('Measured IRF file (scatter PTU or .pck)',      'file'),
+        ('Estimate from decay - raw',                    'raw'),
+        ('Estimate from decay - parametric',             'parametric'),
+        ('Gaussian (fallback)',                          'gaussian'),
+    ]
+    def __init__(self, parent, default='irf_xlsx', xlsx_var=None, machine_irf_default: str = ''):
+        self.xlsx_var = xlsx_var
+        self._machine_irf_default = machine_irf_default
+        self.sv_method = tk.StringVar(value=default)
+        self.sv_path = tk.StringVar()
+        self.frame = _section(parent, 'Instrument Response Function (IRF)',
+                              help_topic='irf')
+        self.frame.columnconfigure(1, weight=1)
+        for i, (lbl, val) in enumerate(self.CHOICES):
+            ttk.Radiobutton(self.frame, text=lbl, variable=self.sv_method,
+                            value=val, command=self._update).grid(
+                row=i, column=0, columnspan=3, sticky='w', padx=4, pady=1)
+        r = len(self.CHOICES)
+        self._path_lbl = ttk.Label(self.frame, text='IRF file')
+        self._path_lbl.grid(row=r, column=0, sticky='e', padx=6, pady=3)
+        self._path_e = ttk.Entry(self.frame, textvariable=self.sv_path, width=45)
+        self._path_e.grid(row=r, column=1, sticky='ew', padx=4, pady=3)
+        self._path_btn = ttk.Button(
+            self.frame, text='Browse...',
+            command=self._browse_irf_path)
+        self._path_btn.grid(row=r, column=2, padx=4, pady=3)
+        self._note = ttk.Label(
+            self.frame,
+            text='Uses the LAS X export entered in Input Files above',
+            foreground='grey')
+        self._note.grid(row=r + 1, column=0, columnspan=3, sticky='w', padx=8, pady=3)
+        self._update()
+    def _browse_irf_path(self):
+        if self.sv_method.get().startswith('machine_irf'):
+            _browse_file(self.sv_path, 'Select machine IRF',
+                         [('NumPy array', '*.npy'), ('All', '*.*')])
+        else:
+            from flimkit.formats import supported_extensions
+            _flim = ' '.join('*' + e for e in supported_extensions())
+            _browse_file(self.sv_path, 'Select IRF file',
+                         [('FLIM / PCK / LAS X export',
+                           _flim + ' *.pck *.xlsx *.csv *.tsv *.txt *.dat *.ascii *.asc'),
+                          ('All', '*.*')])
+    def _show_browse(self):
+        method = self.sv_method.get()
+        self._path_lbl.config(
+            text='Machine IRF (.npy) path' if method.startswith('machine_irf') else 'IRF file')
+        if method.startswith('machine_irf') and not self.sv_path.get().endswith('.npy'):
+            self.sv_path.set(self._machine_irf_default)
+        self._path_lbl.grid()
+        self._path_e.grid()
+        self._path_btn.grid()
+        self._note.grid_remove()
+    def _show_note(self):
+        self._path_lbl.grid_remove()
+        self._path_e.grid_remove()
+        self._path_btn.grid_remove()
+        self._note.grid()
+    def _hide_all(self):
+        self._path_lbl.grid_remove()
+        self._path_e.grid_remove()
+        self._path_btn.grid_remove()
+        self._note.grid_remove()
+    def _update(self):
+        method = self.sv_method.get()
+        if method == 'irf_xlsx':
+            self._show_note() if self.xlsx_var is not None else self._show_browse()
+        elif method in ('file',) or method.startswith('machine_irf'):
+            self._show_browse()
+        else:
+            self._hide_all()
+    def grid(self, **kw):
+        self.frame.grid(**kw)
+
+    def grid_remove(self):
+        self.frame.grid_remove()
+    def get_args(self, xlsx_fallback: Optional[str] = None) -> dict:
+        method = self.sv_method.get()
+        path = self.sv_path.get().strip() or None
+        if method == 'irf_xlsx':
+            xlsx = (self.xlsx_var.get().strip() if self.xlsx_var else None) \
+                   or xlsx_fallback or path
+            return dict(irf=None, irf_xlsx=xlsx, estimate_irf='none', no_xlsx_irf=False, machine_irf=None)
+        elif method.startswith('machine_irf'):
+            return dict(irf=None, irf_xlsx=None, estimate_irf=method, no_xlsx_irf=True, machine_irf=path)
+        elif method == 'file':
+            return dict(irf=path, irf_xlsx=None, estimate_irf='none', no_xlsx_irf=True, machine_irf=None)
+        elif method in ('raw', 'parametric'):
+            return dict(irf=None, irf_xlsx=None, estimate_irf=method, no_xlsx_irf=True, machine_irf=None)
+        else:
+            return dict(irf=None, irf_xlsx=None, estimate_irf='none', no_xlsx_irf=True, machine_irf=None)

flimkit/UI/mode_controller.py

@@ -0,0 +1,118 @@
+from flimkit.UI.roi_tools import RoiAnalysisPanel
+
+
+class ModeController:
+    def __init__(self, builder):
+        self.b = builder
+
+    def switch(self, form_id: str):
+        for btn in self.b._form_buttons.values():
+            btn.state(['!pressed'])
+
+        if form_id in self.b._form_inner_frames:
+            # batch and irf are menu-only - no sidebar button to highlight
+
+            self.b._current_form = form_id
+
+            if form_id == 'fov':
+                self.b._stitch_tabs.grid_remove()
+                if 'phasor' in self.b._form_inner_frames:
+                    self.b._form_inner_frames['phasor'][0].grid_remove()
+                if hasattr(self.b, '_roi_analysis_panel'):
+                    self.b._fov_preview._roi_analysis_panel = self.b._roi_analysis_panel
+
+                fov_frame = self.b._form_inner_frames['fov'][0]
+                fov_frame.grid(row=0, column=0, sticky='nsew')
+                fov_frame.lift()
+                fov_frame.tkraise()
+
+                self.b._analysis_tabs.grid(row=0, column=0, sticky='nsew')
+                self.b._analysis_tabs.lift()
+                self.b._analysis_tabs.tkraise()
+                self.b._analysis_tabs.select(0)
+
+                # update_idletasks avoids re-entrant event processing
+                self.b._fit_settings_tab.update_idletasks()
+                self.b._refresh_scrollable_frame(form_id)
+
+            elif form_id == 'stitch':
+                self.b._analysis_tabs.grid_remove()
+                if 'phasor' in self.b._form_inner_frames:
+                    self.b._form_inner_frames['phasor'][0].grid_remove()
+
+                if 'fov' in self.b._form_inner_frames:
+                    self.b._form_inner_frames['fov'][0].grid_remove()
+
+                stitch_frame = self.b._form_inner_frames['stitch'][0]
+                stitch_frame.grid(row=0, column=0, sticky='nsew')
+                stitch_frame.lift()
+                stitch_frame.tkraise()
+
+                self.b._stitch_tabs.grid(row=0, column=0, sticky='nsew')
+                self.b._stitch_tabs.lift()
+                self.b._stitch_tabs.tkraise()
+
+                if not hasattr(self.b, '_stitch_roi_panel'):
+                    self.b._stitch_roi_panel = RoiAnalysisPanel(self.b._stitch_roi_analysis_frame)
+                    self.b._stitch_roi_panel.app = self.b
+                    self.b._stitch_roi_panel.grid(row=0, column=0, sticky='nsew')
+                    self.b._stitch_roi_panel.fov_preview = self.b._fov_preview
+                    self.b._fov_preview._roi_analysis_panel = self.b._stitch_roi_panel
+
+                self.b._stitch_tabs.select(0)
+
+                # update_idletasks avoids re-entrant event processing
+                self.b._stitch_settings_tab.update_idletasks()
+                self.b._refresh_scrollable_frame(form_id)
+
+            else:
+                self.b._analysis_tabs.grid_remove()
+                self.b._stitch_tabs.grid_remove()
+
+                for fid in ('phasor', 'fov', 'stitch', 'batch', 'irf'):
+                    if fid != form_id and fid in self.b._form_inner_frames:
+                        self.b._form_inner_frames[fid][0].grid_remove()
+
+                if form_id in self.b._form_inner_frames:
+                    selected_frame = self.b._form_inner_frames[form_id][0]
+                    selected_frame.grid(row=0, column=0, sticky='nsew')
+                    selected_frame.lift()
+                    selected_frame.tkraise()
+                    self.b._refresh_scrollable_frame(form_id)
+
+            if form_id == 'phasor':
+                self.b._fov_preview.frame.grid_remove()
+                self.b._phasor_panel.frame.grid()
+                self.b._preview_frame_label.configure(text='  Phasor Analysis  ')
+                if (hasattr(self.b, 'sv_ph_ptu') and hasattr(self.b, 'sv_ptu')
+                        and not self.b.sv_ph_ptu.get().strip()):
+                    fov_ptu = self.b.sv_ptu.get().strip()
+                    if fov_ptu:
+                        self.b.sv_ph_ptu.set(fov_ptu)
+                    if hasattr(self.b, '_irf_fov'):
+                        method = self.b._irf_fov.sv_method.get()
+                        if method == 'irf_xlsx' and hasattr(self.b, 'sv_xlsx'):
+                            xlsx = self.b.sv_xlsx.get().strip()
+                            if xlsx and not self.b.sv_ph_irf.get().strip():
+                                self.b.sv_ph_irf.set(xlsx)
+                        elif method == 'machine_irf':
+                            mirf = self.b._irf_fov.sv_path.get().strip()
+                            if mirf and not self.b.sv_ph_mirf.get().strip():
+                                self.b.sv_ph_mirf.set(mirf)
+            elif form_id in ('batch', 'irf'):
+                self.b._phasor_panel.frame.grid_remove()
+                self.b._fov_preview.frame.grid_remove()
+                label = '  Machine IRF Builder  ' if form_id == 'irf' else '  Batch Processing  '
+                self.b._preview_frame_label.configure(text=label)
+                # Show the IRF plot canvas if it exists (created after first build)
+                if form_id == 'irf' and hasattr(self.b, '_irf_plot_frame'):
+                    self.b._irf_plot_frame.grid()
+            else:
+                self.b._phasor_panel.frame.grid_remove()
+                if hasattr(self.b, '_irf_plot_frame'):
+                    self.b._irf_plot_frame.grid_remove()
+                self.b._fov_preview.frame.grid()
+
+        if hasattr(self.b, 'mode_status'):
+            self.b.mode_status.set(f"Current: {self.b._form_labels.get(form_id, form_id)}")
+            self.b._preview_frame_label.configure(text='  FOV Preview  ')

flimkit/UI/modes/base.py

@@ -0,0 +1,3 @@
+class BaseMode:
+    def __init__(self, builder):
+        self.b = builder

flimkit/UI/modes/batch_mode.py

@@ -0,0 +1,312 @@
+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
+
+
+class BatchMode(BaseMode):
+    def build(self):
+        outer, tab = self.b._form_inner_frames['batch']
+        tab.columnconfigure(0, weight=1)
+
+        self.b.state.sv_batch_mode = tk.StringVar(value='tiled')
+
+        self.b._batch_mode_label = ttk.Label(
+            tab, text='Mode: Multi-Tile ROI Fit',
+            font=('TkDefaultFont', 9, 'bold'), foreground='#555')
+        self.b._batch_mode_label.grid(row=0, column=0, sticky='w', padx=8, pady=(6, 2))
+
+        ff = _section(tab, 'Input / Output')
+        ff.grid(row=1, column=0, sticky='ew', pady=(0, 6))
+        ff.columnconfigure(1, weight=1)
+        self.b.state.sv_batch_xlif_dir = tk.StringVar()
+        self.b.state.sv_batch_ptu_dir = tk.StringVar()
+        self.b.state.sv_batch_out_dir = tk.StringVar()
+
+        self.b._batch_xlif_fr = ttk.Frame(ff)
+        self.b._batch_xlif_fr.grid(row=0, column=0, columnspan=3, sticky='ew')
+        self.b._batch_xlif_fr.columnconfigure(1, weight=1)
+        ttk.Label(self.b._batch_xlif_fr, text='XLIF folder *').grid(
+            row=0, column=0, sticky='e', padx=6, pady=3)
+        ttk.Entry(self.b._batch_xlif_fr, textvariable=self.b.sv_batch_xlif_dir, width=45).grid(
+            row=0, column=1, sticky='ew', padx=4, pady=3)
+        ttk.Button(self.b._batch_xlif_fr, text='Browse...',
+                   command=lambda: _browse_dir(self.b.sv_batch_xlif_dir,
+                                               'Folder of XLIF files')).grid(
+            row=0, column=2, padx=4, pady=3)
+
+        _row(ff, 'PTU folder *',      self.b.sv_batch_ptu_dir,  1,
+             lambda: _browse_dir(self.b.sv_batch_ptu_dir,  'PTU tile directory'))
+
+        self.b._batch_out_fr = ttk.Frame(ff)
+        self.b._batch_out_fr.grid(row=2, column=0, columnspan=3, sticky='ew')
+        self.b._batch_out_fr.columnconfigure(1, weight=1)
+        ttk.Label(self.b._batch_out_fr, text='Output base dir *').grid(
+            row=0, column=0, sticky='e', padx=6, pady=3)
+        ttk.Entry(self.b._batch_out_fr, textvariable=self.b.sv_batch_out_dir, width=45).grid(
+            row=0, column=1, sticky='ew', padx=4, pady=3)
+        ttk.Button(self.b._batch_out_fr, text='Browse...',
+                   command=lambda: _browse_dir(self.b.sv_batch_out_dir,
+                                               'Base output directory')).grid(
+            row=0, column=2, padx=4, pady=3)
+
+        self.b.state.bv_batch_save_beside = tk.BooleanVar(value=False)
+        self.b.state.sv_batch_save_beside_preview = tk.StringVar(value='')
+
+        def _update_beside_preview(*_):
+            ptu = self.b.sv_batch_ptu_dir.get().strip()
+            preview = (ptu.rstrip('/\\') + '/save/') if ptu else '<ptu-dir>/save/'
+            self.b.sv_batch_save_beside_preview.set(preview)
+
+        def _on_save_beside(*_):
+            if self.b.bv_batch_save_beside.get():
+                self.b._batch_out_fr.grid_remove()
+                self.b._batch_beside_preview_lbl.pack(side='left', padx=2)
+                _update_beside_preview()
+            else:
+                self.b._batch_out_fr.grid()
+                self.b._batch_beside_preview_lbl.pack_forget()
+
+        self.b.sv_batch_ptu_dir.trace_add('write', _update_beside_preview)
+
+        beside_fr = ttk.Frame(ff)
+        beside_fr.grid(row=3, column=0, columnspan=3, sticky='w')
+        ttk.Checkbutton(beside_fr, text='Save beside input folder  →',
+                        variable=self.b.bv_batch_save_beside,
+                        command=_on_save_beside).pack(side='left', padx=(4, 0))
+        self.b._batch_beside_preview_lbl = ttk.Label(
+            beside_fr, textvariable=self.b.sv_batch_save_beside_preview,
+            foreground='#5c9bd6')
+        self.b._batch_beside_preview_lbl.pack(side='left', padx=2)
+        self.b._batch_beside_preview_lbl.pack_forget()
+
+        self.b._batch_io_help = ttk.Label(
+            ff, text='One sub-folder per ROI created inside the output base dir.',
+            foreground='grey')
+        self.b._batch_io_help.grid(row=4, column=1, columnspan=2, sticky='w', padx=4)
+
+        fi = _section(tab, 'IRF')
+        fi.grid(row=2, column=0, sticky='ew', pady=(0, 6))
+        fi.columnconfigure(1, weight=1)
+        self.b.state.sv_batch_mirf = tk.StringVar(value=str(_C()['MACHINE_IRF_DEFAULT_PATH']))
+        _row(fi, 'Machine IRF (.npy) *', self.b.sv_batch_mirf, 0,
+             lambda: _browse_file(self.b.sv_batch_mirf, 'Machine IRF',
+                                  [('NumPy', '*.npy'), ('All', '*.*')]))
+
+        fp = _section(tab, 'Fitting Parameters', help_topic='fit_model')
+        fp.grid(row=3, 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_batch = tk.StringVar(value='discrete')
+        ttk.Radiobutton(fp, text='n-exp', variable=self.b.sv_fit_model_batch,
+                        value='discrete').grid(row=0, column=1, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='Gaussian dist.', variable=self.b.sv_fit_model_batch,
+                        value='gaussian').grid(row=0, column=2, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='Lorentzian dist.', variable=self.b.sv_fit_model_batch,
+                        value='lorentzian').grid(row=0, column=3, sticky='w', padx=1)
+        ttk.Radiobutton(fp, text='n-exp tail', variable=self.b.sv_fit_model_batch,
+                        value='tail').grid(row=0, column=4, sticky='w', padx=1)
+
+        self.b.state.iv_nexp_batch = tk.IntVar(value=2)
+        self.b.state.iv_ncomp_dist_batch = tk.IntVar(value=1)
+
+        nexp_frame_batch = ttk.Frame(fp)
+        nexp_frame_batch.grid(row=1, column=0, columnspan=5, sticky='w')
+        ttk.Label(nexp_frame_batch, text='Components:').pack(side='left', padx=(4, 8))
+        for n in (1, 2, 3):
+            ttk.Radiobutton(nexp_frame_batch, text=str(n), variable=self.b.iv_nexp_batch,
+                            value=n).pack(side='left', padx=4)
+
+        dist_frame_batch = ttk.Frame(fp)
+        ttk.Label(dist_frame_batch, text='Components:').pack(side='left', padx=(4, 8))
+        ttk.Radiobutton(dist_frame_batch, text='1 (unimodal)', variable=self.b.iv_ncomp_dist_batch,
+                        value=1).pack(side='left', padx=4)
+        ttk.Radiobutton(dist_frame_batch, text='2 (bimodal)', variable=self.b.iv_ncomp_dist_batch,
+                        value=2).pack(side='left', padx=4)
+
+        def _on_batch_model_change(*_):
+            if self.b.sv_fit_model_batch.get() in ('discrete', 'tail'):
+                dist_frame_batch.grid_remove()
+                nexp_frame_batch.grid(row=1, column=0, columnspan=5, sticky='w')
+            else:
+                nexp_frame_batch.grid_remove()
+                dist_frame_batch.grid(row=1, column=0, columnspan=5, sticky='w')
+        self.b.sv_fit_model_batch.trace_add('write', _on_batch_model_change)
+
+        ttk.Label(fp, text='Fit window (ns):').grid(row=2, column=0, sticky='w', **PAD)
+        self.b.state.sv_batch_tau_min = tk.StringVar(value=str(_C()['Tau_min']))
+        self.b.state.sv_batch_tau_max = tk.StringVar(value=str(_C()['Tau_max']))
+        ttk.Entry(fp, textvariable=self.b.sv_batch_tau_min, width=7).grid(row=2, column=1, padx=4)
+        ttk.Label(fp, text='to').grid(row=2, column=2)
+        ttk.Entry(fp, textvariable=self.b.sv_batch_tau_max, width=7).grid(row=2, column=3, padx=4)
+        ttk.Label(fp, text='ns', foreground='grey').grid(row=2, column=4, padx=4)
+
+        ttk.Label(fp, text='Colour scale (ns):').grid(row=3, column=0, sticky='w', **PAD)
+        self.b.state.sv_batch_tau_lo = tk.StringVar(
+            value='' if _C()['TAU_DISPLAY_MIN'] is None else str(_C()['TAU_DISPLAY_MIN']))
+        self.b.state.sv_batch_tau_hi = tk.StringVar(
+            value='' if _C()['TAU_DISPLAY_MAX'] is None else str(_C()['TAU_DISPLAY_MAX']))
+        ttk.Entry(fp, textvariable=self.b.sv_batch_tau_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_batch_tau_hi, width=7).grid(row=3, column=3, padx=4)
+        ttk.Label(fp, text='ns  (display only)', foreground='grey').grid(row=3, column=4, padx=4)
+
+        freg = _section(tab, 'Tile Registration')
+        freg.grid(row=4, column=0, sticky='ew', pady=(0, 6))
+        self.b._batch_freg = freg
+        self.b.state.bv_batch_register = tk.BooleanVar(value=True)
+        ttk.Checkbutton(freg, text='Phase-correlation registration (fixes stage Y/X drift)',
+                        variable=self.b.bv_batch_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_batch_reg_shift = tk.StringVar(value='120')
+        ttk.Entry(freg, textvariable=self.b.sv_batch_reg_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')
+
+        fm = _section(tab, 'Masking', help_topic='masking')
+        fm.grid(row=5, column=0, sticky='ew', pady=(0, 6))
+        self.b.state.bv_batch_thr = tk.BooleanVar(value=False)
+        self.b.state.sv_batch_thr = tk.StringVar()
+        ttk.Checkbutton(fm, text='Intensity threshold (min photons/px):',
+                        variable=self.b.bv_batch_thr,
+                        command=lambda: _tog(self.b.bv_batch_thr, self.b._batch_thr_e)).grid(
+            row=0, column=0, sticky='w', **PAD)
+        self.b._batch_thr_e = ttk.Entry(fm, textvariable=self.b.sv_batch_thr,
+                                      width=8, state='disabled')
+        self.b._batch_thr_e.grid(row=0, column=1, sticky='w', padx=4)
+        self.b.state.bv_batch_correct_pileup = tk.BooleanVar(value=False)
+        ttk.Checkbutton(fm, text='Apply Coates pile-up correction (recommended if pile-up > 5%)',
+                        variable=self.b.bv_batch_correct_pileup).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_batch_tvb_ptu = tk.StringVar()
+        ttk.Entry(fm, textvariable=self.b.sv_batch_tvb_ptu, width=24).grid(
+            row=2, column=1, sticky='ew', padx=4)
+        ttk.Button(fm, text='Browse...',
+                   command=lambda: _browse_file(self.b.sv_batch_tvb_ptu,
+                                                'Background reference PTU',
+                                                FLIM_FILETYPES)).grid(
+            row=2, column=2, sticky='w', padx=4)
+        ttk.Label(fm, text='(optional: applied to every FOV in the batch)',
+                  foreground='grey').grid(row=3, column=0, columnspan=3, sticky='w', padx=8)
+
+        fexp = _section(tab, 'Image Export')
+        fexp.grid(row=6, column=0, sticky='ew', pady=(0, 6))
+        self.b.state.bv_batch_save_lifetime = tk.BooleanVar(value=True)
+        self.b.state.bv_batch_save_rgb = tk.BooleanVar(value=True)
+        self.b.state.bv_batch_save_intensity = tk.BooleanVar(value=True)
+        self.b.state.bv_batch_save_npy = tk.BooleanVar(value=True)
+        self.b.state.bv_batch_save_ind = tk.BooleanVar(value=False)
+        ttk.Checkbutton(fexp, text='Lifetime image (uint16 TIFF)',
+                        variable=self.b.bv_batch_save_lifetime).grid(row=0, column=0, sticky='w', **PAD)
+        ttk.Checkbutton(fexp, text='Component RGB TIFF',
+                        variable=self.b.bv_batch_save_rgb).grid(row=0, column=1, sticky='w', **PAD)
+        ttk.Checkbutton(fexp, text='Intensity TIFF',
+                        variable=self.b.bv_batch_save_intensity).grid(row=0, column=2, sticky='w', **PAD)
+        ttk.Checkbutton(fexp, text='Raw maps (.npy)',
+                        variable=self.b.bv_batch_save_npy).grid(row=1, column=0, sticky='w', **PAD)
+        ttk.Checkbutton(fexp, text='Individual component maps (τ₁, a₁, τ₂...)',
+                        variable=self.b.bv_batch_save_ind).grid(row=1, column=1, columnspan=2, sticky='w', **PAD)
+        self.b.state.bv_batch_save_stack = tk.BooleanVar(value=True)
+        ttk.Checkbutton(fexp, text='4D stacks - (T, H, W) .npy per map  (timelapse only)',
+                        variable=self.b.bv_batch_save_stack).grid(row=2, column=0, columnspan=3, sticky='w', **PAD)
+        ttk.Label(fexp, text='Lifetime colour scale (ns):').grid(row=3, column=0, sticky='w', **PAD)
+        ttk.Entry(fexp, textvariable=self.b.sv_batch_tau_lo, width=7).grid(row=3, column=1, sticky='w', padx=4)
+        ttk.Label(fexp, text='to').grid(row=3, column=2)
+        ttk.Entry(fexp, textvariable=self.b.sv_batch_tau_hi, width=7).grid(row=3, column=3, sticky='w', padx=4)
+        ttk.Label(fexp, text='ns  (blank = auto)', foreground='grey').grid(row=3, column=4, sticky='w', padx=4)
+        ttk.Label(fexp, text='Gamma (lifetime image):').grid(row=4, column=0, sticky='w', **PAD)
+        self.b.state.sv_batch_gamma = tk.StringVar(value='0.4')
+        ttk.Entry(fexp, textvariable=self.b.sv_batch_gamma, width=5).grid(row=4, column=1, sticky='w', padx=4)
+        ttk.Label(fexp, text='(0.4 = boost dim tissue; 1.0 = linear)',
+                  foreground='grey').grid(row=4, column=2, columnspan=3, sticky='w')
+        ttk.Label(fexp, text='Intensity display max:').grid(row=5, column=0, sticky='w', **PAD)
+        self.b.state.sv_batch_int_max = tk.StringVar()
+        ttk.Entry(fexp, textvariable=self.b.sv_batch_int_max, width=8).grid(row=5, column=1, sticky='w', padx=4)
+        ttk.Label(fexp, text='(blank = auto 99th percentile)',
+                  foreground='grey').grid(row=5, column=2, columnspan=3, sticky='w')
+
+        ttk.Label(fexp, text='Lifetime weighting:').grid(row=6, column=0, sticky='w', **PAD)
+        self.b.state.sv_batch_tau_weighting = tk.StringVar(value='amplitude')
+        ttk.Combobox(fexp, textvariable=self.b.sv_batch_tau_weighting, state='readonly',
+                     values=['amplitude', 'intensity'], width=11).grid(row=6, column=1, sticky='w', padx=4)
+        ttk.Label(fexp, text='(τ map / lifetime image; both raw .npy saved either way)',
+                  foreground='grey').grid(row=6, column=2, columnspan=3, sticky='w')
+
+        ftl = _section(tab, 'Timelapse - Reference Lifetimes')
+        ftl.grid(row=7, column=0, sticky='ew', pady=(0, 6))
+        self.b._batch_tl_fr = ftl
+
+        self.b.state.bv_tl_fix_tau = tk.BooleanVar(value=False)
+        self.b.state.sv_tl_tau1 = tk.StringVar(value='')
+        self.b.state.sv_tl_tau2 = tk.StringVar(value='')
+        self.b.state.sv_tl_tau3 = tk.StringVar(value='')
+
+        ttk.Checkbutton(ftl,
+                        text='Fix reference τ values (skip pooled-decay fit)',
+                        variable=self.b.bv_tl_fix_tau,
+                        command=lambda: _tog_tl_entries()).grid(
+            row=0, column=0, columnspan=6, sticky='w', **PAD)
+
+        self.b._tl_tau_fr = ttk.Frame(ftl)
+        self.b._tl_tau_fr.grid(row=1, column=0, columnspan=6, sticky='w')
+
+        def _make_tau_box(col, sym, var):
+            box = ttk.Frame(self.b._tl_tau_fr)
+            box.grid(row=0, column=col, sticky='w')
+            ttk.Label(box, text=sym).grid(row=0, column=0, sticky='e', padx=(8, 2))
+            e = ttk.Entry(box, textvariable=var, width=8, state='disabled')
+            e.grid(row=0, column=1, padx=4)
+            return box, e
+
+        self.b._tl_tau1_box, self.b._tl_tau1_e = _make_tau_box(0, 'τ₁ (ns):', self.b.sv_tl_tau1)
+        self.b._tl_tau2_box, self.b._tl_tau2_e = _make_tau_box(1, 'τ₂ (ns):', self.b.sv_tl_tau2)
+        self.b._tl_tau3_box, self.b._tl_tau3_e = _make_tau_box(2, 'τ₃ (ns):', self.b.sv_tl_tau3)
+        ttk.Label(self.b._tl_tau_fr, text='(leave blank to fit from pooled data)',
+                  foreground='grey').grid(row=0, column=3, padx=6)
+
+        def _tog_tl_entries():
+            state = 'normal' if self.b.bv_tl_fix_tau.get() else 'disabled'
+            self.b._tl_tau1_e.config(state=state)
+            self.b._tl_tau2_e.config(state=state)
+            self.b._tl_tau3_e.config(state=state)
+
+        def _update_tl_tau_count(*_):
+            n = self.b.iv_nexp_batch.get()
+            (self.b._tl_tau2_box.grid() if n >= 2 else self.b._tl_tau2_box.grid_remove())
+            (self.b._tl_tau3_box.grid() if n >= 3 else self.b._tl_tau3_box.grid_remove())
+
+        self.b.iv_nexp_batch.trace_add('write', _update_tl_tau_count)
+        _update_tl_tau_count()
+        self.b.state.bv_tl_pool_positions = tk.BooleanVar(value=False)
+        ttk.Checkbutton(ftl,
+                        text='Pool all positions for a shared reference τ  '
+                             '(default: each position gets its own τ)',
+                        variable=self.b.bv_tl_pool_positions).grid(
+            row=2, column=0, columnspan=5, sticky='w', **PAD)
+
+        self.b.state.bv_tl_bound_fraction = tk.BooleanVar(value=False)
+        ttk.Checkbutton(ftl,
+                        text='Compute bound fraction  α₂/(α₁+α₂)  '
+                             '(off by default - verify component ordering)',
+                        variable=self.b.bv_tl_bound_fraction).grid(
+            row=3, column=0, columnspan=5, sticky='w', **PAD)
+
+        ftl.grid_remove()
+
+        self.b._expert_banner_batch = ttk.Label(
+            tab, text='⚙  Custom expert settings active',
+            foreground='#e8a838', font=('TkDefaultFont', 9, 'bold'))
+        self.b._expert_banner_batch.grid(row=8, column=0, sticky='w', padx=8)
+        self.b._expert_banner_batch.grid_remove()
+
+        btn_row_batch = ttk.Frame(tab)
+        btn_row_batch.grid(row=9, column=0, pady=8)
+        ttk.Button(btn_row_batch, text='⚙  Expert Settings',
+                   command=self.b._open_expert_settings).pack(side='left', padx=4)
+        self.b._btn_batch = ttk.Button(btn_row_batch, text='▶  Run Batch ROI Fit',
+                                     command=self.b._dispatch_batch)
+        self.b._btn_batch.pack(side='left', padx=4, ipadx=20, ipady=4)