diff --git a/notebooks/correlation/post_acquisition_correlation.ipynb b/notebooks/correlation/post_acquisition_correlation.ipynb
index a5ee7ce25369d3d1cad1a2f9e5f3f25fe13e18c8..5ed09581115b13c86cb5e048552a74058f6c383a 100644
--- a/notebooks/correlation/post_acquisition_correlation.ipynb
+++ b/notebooks/correlation/post_acquisition_correlation.ipynb
@@ -30,7 +30,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
@@ -92,7 +92,7 @@
"filename_fluo = os.path.join(fluo_dir, '20240209_Lsw_060_B36G3.lif')\n",
"filename_nav = os.path.join(serialem_dir, 'navi.nav')\n",
"\n",
- "output_dir = os.path.join('/Volumes/ImageAnalysisHub/malbert/correlative_cryo_em/test2',\n",
+ "output_dir = os.path.join('/Volumes/ImageAnalysisHub/malbert/correlative_cryo_em/test3',\n",
" os.path.basename(exp_dir))\n",
"os.makedirs(output_dir, exist_ok=True)\n",
"\n",
@@ -179,7 +179,7 @@
"tomo_files = os.listdir(serialem_dir)\n",
"tomo_files = sorted([f for f in tomo_files if 'TS' in f and f.endswith('mrc.mdoc')])[:]\n",
"\n",
- "tomo_files = tomo_files[:1] # for test run\n",
+ "tomo_files = tomo_files[:] # for test run\n",
"tomo_files"
]
},
@@ -437,7 +437,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
@@ -449,11 +449,13 @@
"viewer = napari.Viewer()\n",
"\n",
"lds = [viewer_utils.create_image_layer_tuples_from_msim(\n",
- " msim, transform_key='corr',\n",
+ " msim,\n",
+ " transform_key='corr4',\n",
+ " # transform_key='to_correlate',\n",
" ch_name=sorted_nodes[il],\n",
- " colormap='grey' if not il else (\"red\" if 'MMM' in sorted_nodes[il] else (\"green\" if 'Anchor' in sorted_nodes[il] else 'blue')),\n",
+ " colormap='gray' if not il else (\"red\" if 'MMM' in sorted_nodes[il] else (\"green\" if 'Anchor' in sorted_nodes[il] else 'blue')),\n",
" )[0]\n",
- " for il, msim in enumerate(msims_corr[:2])]\n",
+ " for il, msim in enumerate(msims_corr[:])]\n",
"viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, manage_viewer_transformations=False)\n",
"viewer.reset_view()"
]
@@ -505,7 +507,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
@@ -551,7 +553,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
@@ -560,7 +562,7 @@
"\n",
"# align centers\n",
"centers = [si_utils.get_center_of_sim(msi_utils.get_sim_from_msim(msim), transform_key=transform_key)\n",
- " for msim, transform_key in zip([msim_LMM, mxim_fluo], ['corr', 'metadata'])]\n",
+ " for msim, transform_key in zip([msim_LMM, mxim_fluo], ['corr4', 'metadata'])]\n",
"\n",
"centering_affine = param_utils.affine_from_translation(centers[0] - centers[1])\n",
"\n",
@@ -570,7 +572,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
@@ -598,7 +600,7 @@
"import napari\n",
"viewer_affinder = napari.Viewer()\n",
"ld_c = viewer_utils.create_image_layer_tuples_from_msim(msim_LMM,\n",
- " transform_key='corr', colormap='gray', contrast_limits=[0,2000], ch_name='LMM', data_as_array=True)\n",
+ " transform_key='corr4', colormap='gray', contrast_limits=[0,2000], ch_name='LMM', data_as_array=True)\n",
"ld_f = viewer_utils.create_image_layer_tuples_from_msim(mxim_fluo_reg,\n",
" transform_key='metadata_centered', colormap='viridis', contrast_limits=[0,30000], ch_name='fluo', data_as_array=True)\n",
"\n",
@@ -621,7 +623,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
@@ -629,10 +631,17 @@
"fluo_new_affine = viewer_affinder.layers[[l.name for l in viewer_affinder.layers].index('fluo')].affine.affine_matrix\n",
"\n",
"# or use previously obtained affine\n",
+ "\n",
+ "# corr\n",
"# fluo_new_affine = np.array([[ 1.05403374e+00, 1.56244380e-01, -1.26217326e+03],\n",
"# [-1.43810518e-01, 1.08022110e+00, -1.02384343e+03],\n",
"# [ 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])\n",
"\n",
+ "# corr4\n",
+ "fluo_new_affine = np.array([[ 9.63959861e-01, 1.28591366e-01, -1.14593774e+03],\n",
+ " [-1.23220019e-01, 9.70173034e-01, -9.29093874e+02],\n",
+ " [ 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])\n",
+ "\n",
"affine_fluo_to_LMM = np.dot(fluo_new_affine,\n",
" np.linalg.inv(msi_utils.get_transform_from_msim(mxim_fluo_reg, transform_key='metadata_centered')[0]))\n"
]
@@ -661,7 +670,7 @@
"import napari\n",
"viewer = napari.Viewer()\n",
"ld_c = viewer_utils.create_image_layer_tuples_from_msim(msim_LMM,\n",
- " transform_key='corr', colormap='gray', contrast_limits=[0,2000], ch_name='LMM')\n",
+ " transform_key='corr4', colormap='gray', contrast_limits=[0,2000], ch_name='LMM')\n",
"ld_f = viewer_utils.create_image_layer_tuples_from_msim(mxim_fluo,\n",
" transform_key='preregistered', colormap='viridis', contrast_limits=[0,30000], ch_name='fluo')\n",
"\n",
@@ -696,7 +705,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
@@ -728,19 +737,23 @@
"source": [
"# visualize in napari\n",
"\n",
- "# import napari\n",
- "# viewer = napari.Viewer()\n",
- "# ld_c = []\n",
- "# for msim in [msim_LMM]:\n",
- "# ld_c += viewer_utils.create_image_layer_tuples_from_msim(msim,\n",
- "# transform_key='corr', colormap='gray', ch_name='LMM')\n",
- " \n",
- "# ld_f = []\n",
- "# for msim in mxims_fluo_max[:4]:\n",
- "# ld_f += viewer_utils.create_image_layer_tuples_from_msim(msim,\n",
- "# transform_key='preregistered', colormap='gray', ch_name='FM')\n",
+ "import napari\n",
+ "viewer = napari.Viewer()\n",
"\n",
- "# viewer_utils.add_image_layer_tuples_to_viewer(viewer, ld_c + ld_f)"
+ "ld_c = []\n",
+ "for msim in [msim_LMM]:\n",
+ " ld_c += viewer_utils.create_image_layer_tuples_from_msim(msim,\n",
+ " transform_key='corr4', colormap='gray', ch_name='LMM')\n",
+ "\n",
+ "ld_f = []\n",
+ "for msim in mxims_fluo_max[:3]:\n",
+ " ld_f += viewer_utils.create_image_layer_tuples_from_msim(msim,\n",
+ " transform_key='preregistered',\n",
+ " # colormap='gray',\n",
+ " # ch_name='FM',\n",
+ " )\n",
+ "\n",
+ "viewer_utils.add_image_layer_tuples_to_viewer(viewer, ld_c + ld_f)"
]
},
{
@@ -789,15 +802,17 @@
" \n",
" # fluo scenes\n",
" pt_dict['fluo_scenes'] = []\n",
+ " pt_dict['fluo_msims'] = []\n",
" for imxim, mxim in tqdm(enumerate(mxims_fluo_max[:])):\n",
" is_inside = clem_utils.pt_in_mxim(pt,\n",
" msi_utils.multiscale_sel_coords(mxim, {'t': 0}), transform_key='preregistered')#, world_affine=M)\n",
" if not is_inside: continue\n",
" scene = fluo_scenes[imxim]\n",
" pt_dict['fluo_scenes'].append(scene)\n",
+ " # pt_dict['fluo_msims'].append(mxim)\n",
"\n",
" pt_dict['serialem_files'] = []\n",
- "\n",
+ " pt_dict['serialem_msims'] = []\n",
" n = fn\n",
" while len(list(g.out_edges(n))) > 0:\n",
" print(n)\n",
@@ -811,7 +826,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
@@ -825,6 +840,98 @@
" pickle.dump(g, f, pickle.HIGHEST_PROTOCOL)"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## View all modalities in napari"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 71,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# visualize in napari\n",
+ "\n",
+ "import napari\n",
+ "viewer = napari.Viewer()\n",
+ "\n",
+ "serialem_transform_key = 'corr4'\n",
+ "\n",
+ "lds = [viewer_utils.create_image_layer_tuples_from_msim(\n",
+ " msims_corr[0],\n",
+ " transform_key=serialem_transform_key,\n",
+ " ch_name='LMM',\n",
+ " colormap='gray'\n",
+ " )[0]]\n",
+ "ls = viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, manage_viewer_transformations=False)\n",
+ "\n",
+ "# ld_f = [viewer_utils.create_image_layer_tuples_from_msim(msim,\n",
+ "# transform_key='preregistered',\n",
+ "# name_prefix='Fluo_grid',\n",
+ "# )[0] for msim, scene in zip(mxims_fluo_max, fluo_scenes) if 'Merged' in scene]\n",
+ "# ls = viewer_utils.add_image_layer_tuples_to_viewer(viewer, ld_f, manage_viewer_transformations=False)\n",
+ "\n",
+ "for k, pt_dict in pt_dicts.items():\n",
+ "\n",
+ " # if not k == 'TS_01': continue\n",
+ "\n",
+ " serialem_msims = [msims_corr[sorted_nodes.index(sem_file)]\n",
+ " for sem_file in pt_dict['serialem_files'] if not 'LMM' in sem_file]\n",
+ "\n",
+ " fluo_msims = [mxim for imxim, mxim in enumerate(mxims_fluo_max)\n",
+ " if fluo_scenes[imxim] in pt_dict['fluo_scenes'] if not 'Merged' in fluo_scenes[imxim]]\n",
+ "\n",
+ " lds = [viewer_utils.create_image_layer_tuples_from_msim(\n",
+ " msim,\n",
+ " transform_key=serialem_transform_key,\n",
+ " # transform_key='to_correlate',\n",
+ " ch_name=k + ' - SEM - ' + pt_dict['serialem_files'][il],\n",
+ " colormap='gray' if 'LMM' in pt_dict['serialem_files'][il]\n",
+ " else (\"red\" if 'MMM' in pt_dict['serialem_files'][il]\n",
+ " else (\"green\" if 'Anchor' in pt_dict['serialem_files'][il]\n",
+ " else 'blue')),\n",
+ " )[0]\n",
+ " for il, msim in enumerate(serialem_msims[:])]\n",
+ "\n",
+ " ls = viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, manage_viewer_transformations=False)\n",
+ " link_layers(ls, attributes=['visible'])\n",
+ " \n",
+ " ld_f = []\n",
+ " for imsim, msim in enumerate(fluo_msims[:]):\n",
+ " ld_f += viewer_utils.create_image_layer_tuples_from_msim(msim,\n",
+ " transform_key='preregistered',\n",
+ " name_prefix = k + ' - Fluo - ' + pt_dict['fluo_scenes'][imsim],\n",
+ " )\n",
+ "\n",
+ " ls = viewer_utils.add_image_layer_tuples_to_viewer(viewer, ld_f, manage_viewer_transformations=False)\n",
+ " link_layers(ls)\n",
+ "\n",
+ " text = {\n",
+ " 'string': '{string}',\n",
+ " 'size': 8,\n",
+ " 'color': 'white',\n",
+ " 'translation': np.array([-30, 0]),\n",
+ " }\n",
+ "\n",
+ " features = {\n",
+ " 'string': [k],\n",
+ " }\n",
+ "\n",
+ " # show point\n",
+ " viewer.add_points(\n",
+ " [pt_dict['pt']],\n",
+ " features=features,\n",
+ " text=text,\n",
+ " size=20,\n",
+ " face_color='red', edge_color='black', name=k,\n",
+ " )\n",
+ "\n",
+ "viewer.reset_view()"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
@@ -972,7 +1079,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "lswistak_paper_correlation",
+ "display_name": "correlation",
"language": "python",
"name": "python3"
},
@@ -986,7 +1093,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.14"
+ "version": "3.10.16"
}
},
"nbformat": 4,