REL 2023-09-18 2023-10-09 2023-10-09 0000-0002-6998-8403 Aleksandra Filipovska University of Western Australia 6 Verdun Street Perth Western Australia Australia 6009 0000-0002-6998-8403 Aleksandra Filipovska University of Western Australia 6 Verdun Street Perth Western Australia Australia 6009 Lee RG Rudler DL Raven SA Peng L Chopin A Moh ESX McCubbin T Siira SJ Fagan SV DeBono NJ Stentenbach M Browne J Rackham FF Li J Simpson KJ Marcellin E Packer NH Reid GE Padman BS Rackham O Filipovska A National Health and Medical Research Council (NHMRC, Australia) APP 2010332 Australia 434.2 10.6019/EMPIAR-11695 FIB-SEM cell Lee RG Rudler DL Raven SA Peng L Chopin A Moh ESX McCubbin T Siira SJ Fagan SV DeBono NJ Stentenbach M Browne J Rackham FF Li J Simpson KJ Marcellin E Packer NH Reid GE Padman BS Rackham O Filipovska A Nature cell Biology Nat. cell Biol. Unprocessed FIB-SEM slices acquired from Cal51 wt cells (Sample A) /data/SampleA_Cal51_wt/1_RawUnprocessedFrames micrographs - single frame TIFF TIFF 598 1 UNSIGNED BYTE 6144 3.372396 4096 3.372396

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 wt cells (Sample A) /data/SampleA_Cal51_wt/2_PreprocessedAIVEinputs micrographs - multiframe TIFF TIFF 5 598 UNSIGNED BYTE 3002 6.744792 909 6.744792

Inputs used to calculate AIVE results for Cal51 wt cells (Sample A), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

AIVE outputs generated from FIB-SEM data of Cal51 wt cells (Sample A). /data/SampleA_Cal51_wt/3_AIVEoutputs reconstructed volumes TIFF TIFF 51 598 UNSIGNED BYTE 3002 6.744792 909 6.744792

AIVE outputs generated for FIB-SEM data acquired from Cal51 wt cells (Sample A), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

Unprocessed FIB-SEM slices acquired from Cal51 PEX26ko cells (Sample B) /data/SampleB_Cal51_PEX26ko/1_RawUnprocessedFrames micrographs - single frame TIFF TIFF 520 1 UNSIGNED BYTE 6144 3.372396 4096 3.372396

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 PEX26ko cells (Sample B) /data/SampleB_Cal51_PEX26ko/2_PreprocessedAIVEinputs micrographs - multiframe TIFF TIFF 5 520 UNSIGNED BYTE 2884 6.744792 1075 6.744792

Inputs used to calculate AIVE results for Cal51 PEX26ko cells (Sample B), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

AIVE outputs generated from FIB-SEM data of Cal51 PEX26ko cells (Sample B) /data/SampleB_Cal51_PEX26ko/3_AIVEoutputs reconstructed volumes TIFF TIFF 85 520 UNSIGNED BYTE 2884 6.744792 1075 6.744792

AIVE outputs generated for FIB-SEM data acquired from Cal51 PEX26ko cells (Sample B), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

Unprocessed FIB-SEM slices acquired from Cal51 GOLGA5ko cells (Sample C) /data/SampleC_Cal51_GOLGA5KO/1_RawUnprocessedFrames micrographs - single frame TIFF TIFF 520 1 UNSIGNED BYTE 6144 3.372396 4096 3.372396

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA5ko cells (Sample C) /data/SampleC_Cal51_GOLGA5KO/2_PreprocessedAIVEinputs micrographs - multiframe TIFF TIFF 5 527 UNSIGNED BYTE 2579 6.744792 1026 6.744792

Inputs used to calculate AIVE results for Cal51 GOLGA5ko cells (Sample C), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

AIVE outputs generated from FIB-SEM data of Cal51 GOLGA5ko cells (Sample C) /data/SampleC_Cal51_GOLGA5KO/3_AIVEoutputs reconstructed volumes TIFF TIFF 79 527 UNSIGNED BYTE 2579 6.744792 1026 6.744792

AIVE outputs generated for FIB-SEM data acquired from Cal51 GOLGA5ko cells (Sample C), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

Unprocessed FIB-SEM slices acquired from Cal51 GOLGA8Mko cells (Sample D) /data/SampleD_Cal51_GOLGA8MKO/1_RawUnprocessedFrames micrographs - single frame TIFF TIFF 502 1 UNSIGNED BYTE 6144 3.372396 4096 3.372396

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA8Mko cells (Sample D) /data/SampleD_Cal51_GOLGA8MKO/2_PreprocessedAIVEinputs micrographs - multiframe TIFF TIFF 5 502 UNSIGNED BYTE 2922 6.744792 1158 6.744792

Inputs used to calculate AIVE results for Cal51 GOLGA8Mko cells (Sample D), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

AIVE outputs generated from FIB-SEM data of Cal51 GOLGA8Mko cells (Sample D) /data/SampleD_Cal51_GOLGA8MKO/3_AIVEoutputs reconstructed volumes TIFF TIFF 49 502 UNSIGNED BYTE 2922 6.744792 1158 6.744792

AIVE outputs generated for FIB-SEM data acquired from Cal51 GOLGA8Mko cells (Sample D), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

Unprocessed FIB-SEM slices acquired from Cal51 SEC61A2ko cells (Sample E) /data/SampleE_Cal51_SEC61A2KO/1_RawUnprocessedFrames micrographs - single frame TIFF TIFF 528 1 UNSIGNED BYTE 6144 3.372396 4096 3.372396

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC61A2ko cells (Sample E) /data/SampleE_Cal51_SEC61A2KO/2_PreprocessedAIVEinputs micrographs - multiframe TIFF TIFF 5 528 UNSIGNED BYTE 3003 6.744792 1356 6.744792

Inputs used to calculate AIVE results for Cal51 SEC61A2ko cells (Sample E), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

AIVE outputs generated from FIB-SEM data of Cal51 SEC61A2ko cells (Sample E) /data/SampleE_Cal51_SEC61A2KO/3_AIVEoutputs reconstructed volumes TIFF TIFF 60 528 UNSIGNED BYTE 3003 6.744792 1356 6.744792

AIVE outputs generated for FIB-SEM data acquired from Cal51 SEC61A2ko cells (Sample E), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

Unprocessed FIB-SEM slices acquired from Cal51 SEC62ko cells (Sample F) /data/SampleF_Cal51_SEC62KO/1_RawUnprocessedFrames micrographs - single frame TIFF TIFF 654 1 UNSIGNED BYTE 6144 3.372396 4096 3.372396

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC62ko cells (Sample F) /data/SampleF_Cal51_SEC62KO/2_PreprocessedAIVEinputs micrographs - multiframe TIFF TIFF 5 654 UNSIGNED BYTE 2910 6.744792 1236 6.744792

Inputs used to calculate AIVE results for Cal51 SEC62ko cells (Sample F), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

AIVE outputs generated from FIB-SEM data of Cal51 SEC62ko cells (Sample F) /data/SampleF_Cal51_SEC62KO/3_AIVEoutputs reconstructed volumes TIFF TIFF 56 654 UNSIGNED BYTE 2910 6.744792 1236 6.744792

AIVE outputs generated for FIB-SEM data acquired from Cal51 SEC62ko cells (Sample F), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.