diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json
index acca7f46d..f21869894 100644
--- a/bids-validator/bids_validator/rules/file_level_rules.json
+++ b/bids-validator/bids_validator/rules/file_level_rules.json
@@ -525,7 +525,7 @@
   },
 
   "microscopy": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?microscopy[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_sample-[a-zA-Z0-9]+)(?:_chunk-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(((@@@_microscopy_type_@@@)(@@@_microscopy_ext_@@@))|(_photo\\.jpg))$",
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?microscopy[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_sample-[a-zA-Z0-9]+)(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_chunk-[a-zA-Z0-9]+)?(((@@@_microscopy_type_@@@)(@@@_microscopy_ext_@@@))|(_photo\\.jpg))$",
     "tokens": {
       "@@@_microscopy_type_@@@": [
         "_TEM",
@@ -555,7 +555,7 @@
     }
   },
   "microscopy_json": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?microscopy[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_sample-[a-zA-Z0-9]+)?(?:_chunk-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(@@@_microscopy_type_@@@)\\.json$",
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?microscopy[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_sample-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_chunk-[a-zA-Z0-9]+)?(@@@_microscopy_type_@@@)\\.json$",
     "tokens": {
       "@@@_microscopy_type_@@@": [
         "_TEM",
diff --git a/bids-validator/bids_validator/rules/session_level_rules.json b/bids-validator/bids_validator/rules/session_level_rules.json
index a7e5c4c98..36be07e6f 100644
--- a/bids-validator/bids_validator/rules/session_level_rules.json
+++ b/bids-validator/bids_validator/rules/session_level_rules.json
@@ -203,7 +203,7 @@
   },
 
   "microscopy_ses": {
-    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_sample-[a-zA-Z0-9]+)?(?:_chunk-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_microscopy_ses_type_@@@)$",
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_sample-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(?:_chunk-[a-zA-Z0-9]+)?(@@@_microscopy_ses_type_@@@)$",
     "tokens": {
       "@@@_microscopy_ses_type_@@@": [
         "_TEM.json",
diff --git a/bids-validator/bids_validator/rules/top_level_rules.json b/bids-validator/bids_validator/rules/top_level_rules.json
index d3ffe05ac..66a3f01b8 100644
--- a/bids-validator/bids_validator/rules/top_level_rules.json
+++ b/bids-validator/bids_validator/rules/top_level_rules.json
@@ -138,7 +138,7 @@
   },
 
   "microscopy_top": {
-    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:_sample-[a-zA-Z0-9]+)?(?:_chunk-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:@@@_microscopy_top_ext_@@@)$",
+    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:_sample-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_stain-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_chunk-[a-zA-Z0-9]+)?(?:@@@_microscopy_top_ext_@@@)$",
     "tokens": {
       "@@@_microscopy_top_ext_@@@": [
         "_TEM\\.json",